September 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2666: Updated manual builds list with human herpesvi...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fa93a7615636 changeset: 2666:fa93a7615636 user: guru date: Wed Sep 09 11:01:22 2009 -0400 description: Updated manual builds list with human herpesvirus genome. 1 file(s) affected in this change: tool-data/shared/ucsc/manual_builds.txt diffs (8 lines): diff -r 9bbf66f38265 -r fa93a7615636 tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Wed Sep 09 10:08:29 2009 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Wed Sep 09 11:01:22 2009 -0400 @@ -663,3 +663,4 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 chr=4744448 baciAnth_AMES Bacillus anthracis str. Ames chr=5227293 shewOnei Shewanella oneidensis MR-1 plasmid_pMR-1=161613,chr=4969803 +15217 Human herpesvirus 1 NC_001806=152261

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[hg] galaxy 2663: removing debuging statements from annotation_p...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5d92863c4860 changeset: 2663:5d92863c4860 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 04 10:49:02 2009 -0400 description: removing debuging statements from annotation_profiler that were never inteded to go out 1 file(s) affected in this change: tools/annotation_profiler/annotation_profiler_for_interval.py diffs (71 lines): diff -r e929a2d803e4 -r 5d92863c4860 tools/annotation_profiler/annotation_profiler_for_interval.py --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:40:16 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:49:02 2009 -0400 @@ -26,8 +26,7 @@ self.filename = filename self.length = int( self.file_size / self.fmt_size / 2 ) self._cached_ranges = [ None for i in xrange( self.length ) ] - def __getitem__( self, i ): - old_i = i + def __getitem__( self, i ): if self._cached_ranges[i] is not None: return self._cached_ranges[i] if i < 0: i = self.length + i @@ -36,14 +35,8 @@ try: start = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] end = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] - except Exception, e: - print 'filename', self.filename - print 'len', len( self ) - print 'fmtsize', self.fmt_size - print 'index', i - print 'old i', old_i - print 'offset', offset - raise IndexError( str( e ) ) + except Exception, e: + raise IndexError, e self._cached_ranges[i] = ( start, end ) return start, end def __len__( self ): @@ -148,25 +141,21 @@ if chrom not in self.chromosome_coverage: self.chromosome_coverage[chrom] = bx.bitset.BitSet( chrom_length ) - self.chromosome_coverage[chrom].set_range( region_start, region_length ) - try: - for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): - if table_name not in self.table_coverage: - self.table_coverage[table_name] = 0 - self.table_chromosome_size[table_name] = {} - self.table_regions_overlaped_count[table_name] = 0 - self.interval_table_overlap_count[table_name] = 0 - self.table_chromosome_count[table_name] = {} - if chrom not in self.table_chromosome_size[table_name]: - self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage - self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) - self.table_coverage[table_name] += coverage - if coverage: - self.interval_table_overlap_count[table_name] += 1 - self.table_regions_overlaped_count[table_name] += regions - except Exception, e: - print "chrom:%s, start:%s, end%s:." % ( chrom, start, end ) - raise e + self.chromosome_coverage[chrom].set_range( region_start, region_length ) + for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): + if table_name not in self.table_coverage: + self.table_coverage[table_name] = 0 + self.table_chromosome_size[table_name] = {} + self.table_regions_overlaped_count[table_name] = 0 + self.interval_table_overlap_count[table_name] = 0 + self.table_chromosome_count[table_name] = {} + if chrom not in self.table_chromosome_size[table_name]: + self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage + self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) + self.table_coverage[table_name] += coverage + if coverage: + self.interval_table_overlap_count[table_name] += 1 + self.table_regions_overlaped_count[table_name] += regions def iter_table_coverage( self ): def get_nr_coverage(): #returns non-redundant coverage, where user's input intervals have been collapse to resolve overlaps

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[hg] galaxy 2662: First pass at allowing MAF tools to deal with ...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e929a2d803e4 changeset: 2662:e929a2d803e4 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 04 10:40:16 2009 -0400 description: First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary. These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index. A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once. 29 file(s) affected in this change: lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml lib/galaxy/datatypes/converters/maf_to_interval_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.xml lib/galaxy/datatypes/sequence.py lib/galaxy/tools/util/maf_utilities.py test-data/cf_maf2fasta_new.dat test-data/maf_split_by_species_collapsed_out.maf test-data/maf_split_by_species_in.maf test-data/maf_split_by_species_not_collapsed_out.maf tool_conf.xml.sample tools/annotation_profiler/annotation_profiler_for_interval.py tools/maf/genebed_maf_to_fasta.xml tools/maf/interval2maf.py tools/maf/interval2maf.xml tools/maf/interval2maf_pairwise.xml tools/maf/interval_maf_to_merged_fasta.py tools/maf/interval_maf_to_merged_fasta.xml tools/maf/maf_filter.py tools/maf/maf_limit_size.py tools/maf/maf_limit_size.xml tools/maf/maf_limit_to_species.py tools/maf/maf_split_by_species.py tools/maf/maf_split_by_species.xml tools/maf/maf_stats.py tools/maf/maf_stats.xml tools/maf/maf_to_fasta.xml tools/maf/maf_to_fasta_concat.py tools/maf/maf_to_fasta_multiple_sets.py diffs (1927 lines): diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/datatypes/converters/maf_to_fasta_converter.py --- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py Fri Sep 04 10:40:16 2009 -0400 @@ -14,12 +14,15 @@ input_name = sys.argv.pop(1) out = open( output_name, 'w' ) count = 0 - for count, maf in enumerate( bx.align.maf.Reader( open( input_name, 'r' ) ) ): - for c in maf.components: - spec, chrom = bx.align.maf.src_split( c.src ) - if not spec or not chrom: - spec = chrom = c.src - out.write( "%s\n" % maf_utilities.get_fasta_header( c, suffix = "%s_%i" % ( spec, count ) ) ) + for count, block in enumerate( bx.align.maf.Reader( open( input_name, 'r' ) ) ): + spec_counts = {} + for c in block.components: + spec, chrom = maf_utilities.src_split( c.src ) + if spec not in spec_counts: + spec_counts[ spec ] = 0 + else: + spec_counts[ spec ] += 1 + out.write( "%s\n" % maf_utilities.get_fasta_header( c, { 'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, count, spec_counts[ spec ] ) ) ) out.write( "%s\n" % c.text ) out.write( "\n" ) out.close() @@ -27,3 +30,12 @@ if __name__ == "__main__": __main__() + + for component in block.components: + spec, chrom = maf_utilities.src_split( component.src ) + if spec not in spec_counts: + spec_counts[ spec ] = 0 + else: + spec_counts[ spec ] += 1 + file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) ) + file_out.write( "%s\n" % component.text ) diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="CONVERTER_maf_to_fasta_0" name="Convert MAF to Fasta"> +<tool id="CONVERTER_maf_to_fasta_0" name="Convert MAF to Fasta" version="1.0.1">  <command interpreter="python">maf_to_fasta_converter.py $output1 $input1</command> <inputs> diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/datatypes/converters/maf_to_interval_converter.py --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Fri Sep 04 10:40:16 2009 -0400 @@ -4,7 +4,8 @@ import sys from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) -import bx.align.maf +import bx.align.maf +from galaxy.tools.util import maf_utilities assert sys.version_info[:2] >= ( 2, 4 ) @@ -17,15 +18,15 @@ #write interval header line out.write( "#chrom\tstart\tend\tstrand\n" ) try: - for maf in bx.align.maf.Reader( open(input_name, 'r') ): - c = maf.get_component_by_src_start(species) - if c is not None: - out.write( "%s\t%i\t%i\t%s\n" % (bx.align.src_split(c.src)[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand) ) - count += 1 + for block in bx.align.maf.Reader( open( input_name, 'r' ) ): + for c in maf_utilities.iter_components_by_src_start( block, species ): + if c is not None: + out.write( "%s\t%i\t%i\t%s\n" % ( bx.align.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) ) + count += 1 except Exception, e: print >> sys.stderr, "There was a problem processing your input: %s" % e out.close() - print "%i MAF blocks converted to Genomic Intervals for species %s." % (count, species) + print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species ) if __name__ == "__main__": __main__() diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/datatypes/converters/maf_to_interval_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals"> +<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.1">  <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> <inputs> diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/datatypes/sequence.py Fri Sep 04 10:40:16 2009 -0400 @@ -22,7 +22,7 @@ pass class Alignment( Sequence ): - """Class describing an alignmnet""" + """Class describing an alignment""" """Add metadata elements""" MetadataElement( name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None ) @@ -316,6 +316,78 @@ import bx.align.maf except: pass +#trying to import maf_utilities here throws an ImportError due to a circular import between jobs and tools: +#from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes +#Traceback (most recent call last): +# File "./scripts/paster.py", line 27, in <module> +# command.run() +# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 78, in run +# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 117, in invoke +# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/command.py", line 212, in run +# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/serve.py", line 227, in command +# File "build/bdist.solaris-2.11-i86pc/egg/paste/script/serve.py", line 250, in loadapp +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 193, in loadapp +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 213, in loadobj +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 237, in loadcontext +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 267, in _loadconfig +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 397, in get_context +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 439, in _context_from_explicit +# File "build/bdist.solaris-2.11-i86pc/egg/paste/deploy/loadwsgi.py", line 18, in import_string +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/pkg_resources.py", line 1912, in load +# entry = __import__(self.module_name, globals(),globals(), ['__name__']) +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/web/buildapp.py", line 18, in <module> +# from galaxy import config, jobs, util, tools +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/jobs/__init__.py", line 3, in <module> +# from galaxy import util, model +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/model/__init__.py", line 13, in <module> +# import galaxy.datatypes.registry +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/datatypes/registry.py", line 6, in <module> +# import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/datatypes/sequence.py", line 344, in <module> +# from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes +# File "/afs/bx.psu.edu/home/dan/galaxy/central/lib/galaxy/tools/__init__.py", line 15, in <module> +# from galaxy import util, jobs, model +#ImportError: cannot import name jobs +#so we'll copy and paste for now...terribly icky +#*** ANYCHANGE TO THIS METHOD HERE OR IN maf_utilities MUST BE PROPAGATED *** +def COPIED_build_maf_index_species_chromosomes( filename, index_species = None ): + species = [] + species_chromosomes = {} + indexes = bx.interval_index_file.Indexes() + try: + maf_reader = bx.align.maf.Reader( open( filename ) ) + while True: + pos = maf_reader.file.tell() + block = maf_reader.next() + if block is None: break + for c in block.components: + spec = c.src + chrom = None + if "." in spec: + spec, chrom = spec.split( ".", 1 ) + if spec not in species: + species.append( spec ) + species_chromosomes[spec] = [] + if chrom and chrom not in species_chromosomes[spec]: + species_chromosomes[spec].append( chrom ) + if index_species is None or spec in index_species: + forward_strand_start = c.forward_strand_start + forward_strand_end = c.forward_strand_end + try: + forward_strand_start = int( forward_strand_start ) + forward_strand_end = int( forward_strand_end ) + except ValueError: + continue #start and end are not integers, can't add component to index, goto next component + #this likely only occurs when parse_e_rows is True? + #could a species exist as only e rows? should the + if forward_strand_end > forward_strand_start: + #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed + indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size ) + except Exception, e: + #most likely a bad MAF + log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) ) + return ( None, [], {} ) + return ( indexes, species, species_chromosomes ) class Maf( Alignment ): """Class describing a Maf alignment""" @@ -333,38 +405,8 @@ Parses and sets species, chromosomes, index from MAF file. """ #these metadata values are not accessable by users, always overwrite + indexes, species, species_chromosomes = COPIED_build_maf_index_species_chromosomes( dataset.file_name ) - try: - maf_reader = bx.align.maf.Reader( open( dataset.file_name ) ) - except: - return #not a maf file - species = [] - species_chromosomes = {} - indexes = bx.interval_index_file.Indexes() - while True: - pos = maf_reader.file.tell() - block = maf_reader.next() - if block is None: break - for c in block.components: - spec = c.src - chrom = None - if "." in spec: - spec, chrom = spec.split( ".", 1 ) - if spec not in species: - species.append(spec) - species_chromosomes[spec] = [] - if chrom and chrom not in species_chromosomes[spec]: - species_chromosomes[spec].append( chrom ) - forward_strand_start = c.forward_strand_start - forward_strand_end = c.forward_strand_end - try: - forward_strand_start = int( forward_strand_start ) - forward_strand_end = int( forward_strand_end ) - except ValueError: - continue #start and end are not integers, can't add component to index, goto next component - if forward_strand_end > forward_strand_start: - #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed - indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size ) dataset.metadata.species = species #only overwrite the contents if our newly determined chromosomes don't match stored chrom_file = dataset.metadata.species_chromosomes diff -r 99dcba7af5b6 -r e929a2d803e4 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Fri Sep 04 10:31:23 2009 -0400 +++ b/lib/galaxy/tools/util/maf_utilities.py Fri Sep 04 10:40:16 2009 -0400 @@ -7,10 +7,41 @@ import bx.align.maf import bx.intervals import bx.interval_index_file -import sys, os, string, tempfile +import sys, os, string, tempfile +import logging +from copy import deepcopy assert sys.version_info[:2] >= ( 2, 4 ) - + +log = logging.getLogger(__name__) + + +GAP_CHARS = [ '-' ] +SRC_SPLIT_CHAR = '.' + +def src_split( src ): + spec, chrom = bx.align.maf.src_split( src ) + if None in [ spec, chrom ]: + spec = chrom = src + return spec, chrom + +def src_merge( spec, chrom, contig = None ): + if None in [ spec, chrom ]: + spec = chrom = spec or chrom + return bx.align.maf.src_merge( spec, chrom, contig ) + +def get_species_in_block( block ): + species = [] + for c in block.components: + spec, chrom = src_split( c.src ) + if spec not in species: + species.append( spec ) + return species + +def tool_fail( msg = "Unknown Error" ): + print >> sys.stderr, "Fatal Error: %s" % msg + sys.exit() + #an object corresponding to a reference layered alignment class RegionAlignment( object ): @@ -153,69 +184,187 @@ except: return build_maf_index( maf_file, species = species ) +#*** ANYCHANGE TO THIS METHOD HERE OR IN galaxy.datatypes.sequences MUST BE PROPAGATED *** +def build_maf_index_species_chromosomes( filename, index_species = None ): + species = [] + species_chromosomes = {} + indexes = bx.interval_index_file.Indexes() + try: + maf_reader = bx.align.maf.Reader( open( filename ) ) + while True: + pos = maf_reader.file.tell() + block = maf_reader.next() + if block is None: break + for c in block.components: + spec = c.src + chrom = None + if "." in spec: + spec, chrom = spec.split( ".", 1 ) + if spec not in species: + species.append( spec ) + species_chromosomes[spec] = [] + if chrom and chrom not in species_chromosomes[spec]: + species_chromosomes[spec].append( chrom ) + if index_species is None or spec in index_species: + forward_strand_start = c.forward_strand_start + forward_strand_end = c.forward_strand_end + try: + forward_strand_start = int( forward_strand_start ) + forward_strand_end = int( forward_strand_end ) + except ValueError: + continue #start and end are not integers, can't add component to index, goto next component + #this likely only occurs when parse_e_rows is True? + #could a species exist as only e rows? should the + if forward_strand_end > forward_strand_start: + #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed + indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size ) + except Exception, e: + #most likely a bad MAF + log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) ) + return ( None, [], {} ) + return ( indexes, species, species_chromosomes ) #builds and returns ( index, index_filename ) for specified maf_file def build_maf_index( maf_file, species = None ): - indexes = bx.interval_index_file.Indexes() - try: - maf_reader = bx.align.maf.Reader( open( maf_file ) ) - # Need to be a bit tricky in our iteration here to get the 'tells' right - while True: - pos = maf_reader.file.tell() - block = maf_reader.next() - if block is None: break - for c in block.components: - if species is not None and c.src.split( "." )[0] not in species: - continue - indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos ) + indexes, found_species, species_chromosomes = build_maf_index_species_chromosomes( maf_file, species ) + if indexes is not None: fd, index_filename = tempfile.mkstemp() out = os.fdopen( fd, 'w' ) indexes.write( out ) out.close() - return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), index_filename ) - except: - return ( None, None ) - -def chop_block_by_region( block, src, region, species = None, mincols = 0, force_strand = None ): - ref = block.get_component_by_src( src ) - #We want our block coordinates to be from positive strand - if ref.strand == "-": - block = block.reverse_complement() - ref = block.get_component_by_src( src ) + return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), index_filename ) + return ( None, None ) + +def component_overlaps_region( c, region ): + if c is None: return False + start, end = c.get_forward_strand_start(), c.get_forward_strand_end() + if region.start >= end or region.end <= start: + return False + return True + +def chop_block_by_region( block, src, region, species = None, mincols = 0 ): + # This chopping method was designed to maintain consistency with how start/end padding gaps have been working in Galaxy thus far: + # behavior as seen when forcing blocks to be '+' relative to src sequence (ref) and using block.slice_by_component( ref, slice_start, slice_end ) + # whether-or-not this is the 'correct' behavior is questionable, but this will at least maintain consistency + # comments welcome + slice_start = block.text_size #max for the min() + slice_end = 0 #min for the max() + old_score = block.score #save old score for later use + # We no longer assume only one occurance of src per block, so we need to check them all + for c in iter_components_by_src( block, src ): + if component_overlaps_region( c, region ): + if c.text is not None: + rev_strand = False + if c.strand == "-": + #We want our coord_to_col coordinates to be returned from positive stranded component + rev_strand = True + c = c.reverse_complement() + start = max( region.start, c.start ) + end = min( region.end, c.end ) + start = c.coord_to_col( start ) + end = c.coord_to_col( end ) + if rev_strand: + #need to orient slice coordinates to the original block direction + slice_len = end - start + end = len( c.text ) - start + start = end - slice_len + slice_start = min( start, slice_start ) + slice_end = max( end, slice_end ) + + if slice_start < slice_end: + block = block.slice( slice_start, slice_end ) + if block.text_size > mincols: + # restore old score, may not be accurate, but it is better than 0 for everything? + block.score = old_score + if species is not None: + block = block.limit_to_species( species ) + block.remove_all_gap_columns() + return block + return None - #save old score here for later use - old_score = block.score - slice_start = max( region.start, ref.start ) - slice_end = min( region.end, ref.end ) - - #slice block by reference species at determined limits - block = block.slice_by_component( ref, slice_start, slice_end ) - - if block.text_size > mincols: - if ( force_strand is None and region.strand != ref.strand ) or ( force_strand is not None and force_strand != ref.strand ): - block = block.reverse_complement() - # restore old score, may not be accurate, but it is better than 0 for everything - block.score = old_score - if species is not None: - block = block.limit_to_species( species ) - block.remove_all_gap_columns() - return block - return None +def orient_block_by_region( block, src, region, force_strand = None ): + #loop through components matching src, + #make sure each of these components overlap region + #cache strand for each of overlaping regions + #if force_strand / region.strand not in strand cache, reverse complement + ### we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing + strands = [ c.strand for c in iter_components_by_src( block, src ) if component_overlaps_region( c, region ) ] + if strands and ( force_strand is None and region.strand not in strands ) or ( force_strand is not None and force_strand not in strands ): + block = block.reverse_complement() + return block + +def get_oriented_chopped_blocks_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): + for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols, force_strand ): + yield block +def get_oriented_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols ): + yield orient_block_by_region( block, src, region, force_strand ), idx, offset + +#split a block with multiple occurances of src into one block per src +def iter_blocks_split_by_src( block, src ): + for src_c in iter_components_by_src( block, src ): + new_block = bx.align.Alignment( score=block.score, attributes=deepcopy( block.attributes ) ) + new_block.text_size = block.text_size + for c in block.components: + if c == src_c or c.src != src: + new_block.add_component( deepcopy( c ) ) #components have reference to alignment, dont want to loose reference to original alignment block in original components + yield new_block + +#split a block into multiple blocks with all combinations of a species appearing only once per block +def iter_blocks_split_by_species( block, species = None ): + def __split_components_by_species( components_by_species, new_block ): + if components_by_species: + #more species with components to add to this block + components_by_species = deepcopy( components_by_species ) + spec_comps = components_by_species.pop( 0 ) + for c in spec_comps: + newer_block = deepcopy( new_block ) + newer_block.add_component( deepcopy( c ) ) + for value in __split_components_by_species( components_by_species, newer_block ): + yield value + else: + #no more components to add, yield this block + yield new_block + + #divide components by species + spec_dict = {} + if not species: + species = [] + for c in block.components: + spec, chrom = src_split( c.src ) + if spec not in spec_dict: + spec_dict[ spec ] = [] + species.append( spec ) + spec_dict[ spec ].append( c ) + else: + for spec in species: + spec_dict[ spec ] = [] + for c in iter_components_by_src_start( block, spec ): + spec_dict[ spec ].append( c ) + + empty_block = bx.align.Alignment( score=block.score, attributes=deepcopy( block.attributes ) ) #should we copy attributes? + empty_block.text_size = block.text_size + #call recursive function to split into each combo of spec/blocks + for value in __split_components_by_species( spec_dict.values(), empty_block ): + sort_block_components_by_block( value, block ) #restore original component order + yield value + + #generator yielding only chopped and valid blocks for a specified region -def get_chopped_blocks_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): - for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols, force_strand ): +def get_chopped_blocks_for_region( index, src, region, species = None, mincols = 0 ): + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region( index, src, region, species, mincols ): yield block -def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0, force_strand = None ): +def get_chopped_blocks_with_index_offset_for_region( index, src, region, species = None, mincols = 0 ): for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, region.start, region.end ): - block = chop_block_by_region( block, src, region, species, mincols, force_strand ) + block = chop_block_by_region( block, src, region, species, mincols ) if block is not None: yield block, idx, offset #returns a filled region alignment for specified regions -def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0 ): +def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): if species is not None: alignment = RegionAlignment( end - start, species ) else: alignment = RegionAlignment( end - start, primary_species ) - return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols ) + return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps ) #reduces a block to only positions exisiting in the src provided def reduce_block_by_primary_genome( block, species, chromosome, region_start ): @@ -237,13 +386,11 @@ return ( start_offset, species_texts ) #fills a region alignment -def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0 ): +def fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): region = bx.intervals.Interval( start, end ) region.chrom = chrom region.strand = strand primary_src = "%s.%s" % ( primary_species, chrom ) - - #Order blocks overlaping this position by score, lowest first blocks = [] @@ -255,28 +402,40 @@ break else: blocks.append( ( score, idx, offset ) ) - + + gap_chars_tuple = tuple( GAP_CHARS ) + gap_chars_str = ''.join( GAP_CHARS ) #Loop through ordered blocks and layer by increasing score - for block_dict in blocks: - block = chop_block_by_region( block_dict[1].get_at_offset( block_dict[2] ), primary_src, region, species, mincols, strand ) - if block is None: continue - start_offset, species_texts = reduce_block_by_primary_genome( block, primary_species, chrom, start ) - for spec, text in species_texts.items(): - try: - alignment.set_range( start_offset, spec, text ) - except: - #species/sequence for species does not exist - pass - + for block_dict in blocks: for block in iter_blocks_split_by_species( block_dict[1].get_at_offset( block_dict[2] ) ): #need to handle each occurance of sequence in block seperately + if component_overlaps_region( block.get_component_by_src( primary_src ), region ): + block = chop_block_by_region( block, primary_src, region, species, mincols ) #chop block + block = orient_block_by_region( block, primary_src, region ) #orient block + start_offset, species_texts = reduce_block_by_primary_genome( block, primary_species, chrom, start ) + for spec, text in species_texts.items(): + #we should trim gaps from both sides, since these are not positions in this species genome (sequence) + text = text.rstrip( gap_chars_str ) + gap_offset = 0 + while text.startswith( gap_chars_tuple ): + gap_offset += 1 + text = text[1:] + if not text: + break + if text: + if overwrite_with_gaps: + alignment.set_range( start_offset + gap_offset, spec, text ) + else: + for i, char in enumerate( text ): + if char not in GAP_CHARS: + alignment.set_position( start_offset + gap_offset + i, spec, char ) return alignment #returns a filled spliced region alignment for specified region with start and end lists -def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0 ): +def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): #create spliced alignment object if species is not None: alignment = SplicedAlignment( starts, ends, species ) else: alignment = SplicedAlignment( starts, ends, [primary_species] ) for exon in alignment.exons: - fill_region_alignment( exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols) + fill_region_alignment( exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps ) return alignment #loop through string array, only return non-commented lines @@ -319,29 +478,36 @@ starts.append( start ) ends.append( end ) return ( starts, ends, fields ) - -def get_species_in_maf( maf_filename ): - try: - species={} - - file_in = open( maf_filename, 'r' ) - maf_reader = maf.Reader( file_in ) - - for i, m in enumerate( maf_reader ): - l = m.components - for c in l: - spec, chrom = maf.src_split( c.src ) - if not spec or not chrom: - spec = chrom = c.src - species[spec] = spec - - file_in.close() - - species = species.keys() - species.sort() - return species - except: - return [] + +def iter_components_by_src( block, src ): + for c in block.components: + if c.src == src: + yield c + +def get_components_by_src( block, src ): + return [ value for value in iter_components_by_src( block, src ) ] + +def iter_components_by_src_start( block, src ): + for c in block.components: + if c.src.startswith( src ): + yield c + +def get_components_by_src_start( block, src ): + return [ value for value in iter_components_by_src_start( block, src ) ] + +def sort_block_components_by_block( block1, block2 ): + #orders the components in block1 by the index of the component in block2 + #block1 must be a subset of block2 + #occurs in-place + return block1.components.sort( cmp = lambda x, y: block2.components.index( x ) - block2.components.index( y ) ) + +def get_species_in_maf( maf_filename ): + species = [] + for block in maf.Reader( open( maf_filename ) ): + for spec in get_species_in_block( block ): + if spec not in species: + species.append( spec ) + return species def parse_species_option( species ): if species: diff -r 99dcba7af5b6 -r e929a2d803e4 test-data/cf_maf2fasta_new.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cf_maf2fasta_new.dat Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,134 @@ +>hg17.chr7(+):127471195-127471526|sequence_index=0|block_index=0|species=hg17|hg17_0_0 +gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA +>panTro1.chr6(+):129885076-129885407|sequence_index=0|block_index=0|species=panTro1|panTro1_0_0 +gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA +>rheMac2.chr3(+):165787989-165788319|sequence_index=0|block_index=0|species=rheMac2|rheMac2_0_0 +gcttgccatcttttgatgctcttgggaatccagcagctgtcaccat-taaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCATAGGCAtgagtcaggccatagtgctggacccacagaattatgagctaaataagtagtgttgggttaagtcactaagttttaggcatagtgtgttatgtagcTCACAAACATATAAGACTGTGTGTTTTTTGACTGGAGGAAGAGATGCCATAAAGACCACCTTTTGAAACTTCTCAAATACTGCCATTGATGTGCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA +>rn3.chr4(+):56178191-56178473|sequence_index=0|block_index=0|species=rn3|rn3_0_0 +CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCTGT----CAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTCGG-AGTCTAGCTGTAGACAGCCCAATGGG---------------------------------------------------------TATAAC---------AATACTCACTAA +>mm7.chr6(+):28984529-28984886|sequence_index=0|block_index=0|species=mm7|mm7_0_0 +CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAACG-AGGGTGGTCCAGTTACTATCTTG---ACTGCAGCTGG----CAGTCAGTTGCCACT--CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCC-AGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA + +>hg17.chr7(+):127471526-127471584|sequence_index=0|block_index=1|species=hg17|hg17_1_0 +AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG +>mm7.chr6(+):28984886-28984940|sequence_index=0|block_index=1|species=mm7|mm7_1_0 +----AACGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG +>rheMac2.chr3(+):165788319-165788377|sequence_index=0|block_index=1|species=rheMac2|rheMac2_1_0 +AATTTGTGGTTTATTTATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG +>panTro1.chr6(+):129885407-129885465|sequence_index=0|block_index=1|species=panTro1|panTro1_1_0 +AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG + +>hg17.chr7(+):127471584-127471688|sequence_index=0|block_index=2|species=hg17|hg17_2_0 +GAGATATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggaattattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt +>panTro1.chr6(+):129885465-129885569|sequence_index=0|block_index=2|species=panTro1|panTro1_2_0 +GAGACATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggagttattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt +>rheMac2.chr3(+):165788377-165788482|sequence_index=0|block_index=2|species=rheMac2|rheMac2_2_0 +GAGATATTT-GGggaaatttg-gtatagactagctt--tcatgatgtaagggagttatttttgtgtgataatggccctacagttac-acagaaattcttccttatttttt +>canFam2.chr14(-):11090703-11090811|sequence_index=0|block_index=2|species=canFam2|canFam2_2_0 +gagatattt-gggggaatttgaatgtagtgttgctcttttgtgatgctaagaaattataattgtctgatgatagtctcgtggttatgggggaaatgcttcctta-ttttt +>bosTau2.chr4(-):50243931-50244034|sequence_index=0|block_index=2|species=bosTau2|bosTau2_2_0 +-agacattg-ggtaaaattcaaatgcagactagctc----atgatgttaaagaattactcttgtgtggtaatggtcttgtgatagagatagaaatgcttcctta-ttttt +>rn3.chr4(+):56182200-56182295|sequence_index=0|block_index=2|species=rn3|rn3_2_0 +----TATTTGGGGGAAATATG-ATGTGCA----CTT--CCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAA-ATAAAAAAAAT--CTTA-GTTGT +>dasNov1.scaffold_256527(+):298-392|sequence_index=0|block_index=2|species=dasNov1|dasNov1_2_0 +GAGACATTT-GGAGAAATTTG-----------Aatt--tcatgatgttaaggaattacttttgtatgatgatggtcttgtggctat-gtagaatttcttccgtg-tttta + +>hg17.chr7(+):127471688-127471871|sequence_index=0|block_index=3|species=hg17|hg17_3_0 +tgggaagcaccaaagta-------gggataaaatgtcatgatgtgtgcaatacactttaaaatgtttttgccaaaa----------taattaa-------------------------tgaagc--aaatatg---gaaaataataattattaaatctaggt-----gatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcattta--------------------------aaaa- +>panTro1.chr6(+):129885569-129885752|sequence_index=0|block_index=3|species=panTro1|panTro1_3_0 +tgggaaacaccaaagta-------gggataaaatgtcatgatgtgtgcaatacgctttaaaatatttttgccaaaa----------taattaa-------------------------tgaagc--aaatatg---gaaaataataattattaaatctaggt-----gatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcattta--------------------------aaaa- +>rheMac2.chr3(+):165788482-165788684|sequence_index=0|block_index=3|species=rheMac2|rheMac2_3_0 +tgggaagcacaaaagta-------gggataaaatgtcatgatgtgtacaatatgctttaaaatatttttgccaaaa----------taattaa-------------------------tgaagc--aaatatg---gaaaataataactgttaaatctaggt-----gttgggtatattgcagttcattatgttattgcacacttttctgtgtgtttaaaattttcatttaaaaatatgttttaaaaatg-------aaaa- +>rn3.chr4(+):56182295-56182489|sequence_index=0|block_index=3|species=rn3|rn3_3_0 +TAGAAAATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAGATTTTT-----AAA----------TATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATG---GGAAGTGGTAATTGTTACATATGGGT-----AATAAGTAT-----AATTCGTTATATTAT-------TTTTC------TTAGAATTTTTCATTTG--------------------------AAAA- +>bosTau2.chr4(-):50243792-50243930|sequence_index=0|block_index=3|species=bosTau2|bosTau2_3_0 +agataaacacttaagtattta---aggatgaaacgccctgatgtttgtaatttgctttagaatattttagccaaaa----------gaattaa-------------------------tgatgc--aaatatg--caaaaagagta--cgttaaacctaa-----------------------------------------------------atttgCGATTttcattta--------------------------aaaa- +>canFam2.chr14(-):11090345-11090505|sequence_index=0|block_index=3|species=canFam2|canFam2_3_0 +agacacaaactgaagtattta---aggatgaaatgtcatgatgtttgcaattggctttaaaatattttagccaaaa-----------agtaaa-------------------------tgaagc--AAATATG--GGAAGACAATAATCATTAAATCTAGGT-----GATGCATAC---------------------------TTTTCCATATGTTTGAAATTTTCATTTA--------------------------AAAA- +>dasNov1.scaffold_256527(+):393-625|sequence_index=0|block_index=3|species=dasNov1|dasNov1_3_0 +agacgcatgctgaagcatgta---aggataaaatgtcgtggtgtttgtaatttattctaaaacattttagccaaaaacaaataaataaataaa-------------------------tgaagc--aaatatgggggaaatgtttaattgttaaatctagatttaacacggtatataccgtgcttcattatactagtctctacttttccatgtgtttgaaattttCATTAAAATGTTTGTTTGTTGTCTGTTTTAATGAAAT + +>hg17.chr7(+):127471871-127471910|sequence_index=0|block_index=4|species=hg17|hg17_4_0 +actttgagctagacaccaggctatgagcta-ggagcatag +>rheMac2.chr3(+):165788684-165788723|sequence_index=0|block_index=4|species=rheMac2|rheMac2_4_0 +actttgagctagataccaggttatgagcta-ggagcatag +>panTro1.chr6(+):129885752-129885791|sequence_index=0|block_index=4|species=panTro1|panTro1_4_0 +actttgagctagacaccaggctatgagcta-ggagcatag +>bosTau2.chr4(-):50243734-50243773|sequence_index=0|block_index=4|species=bosTau2|bosTau2_4_0 +tcttcgtgcaacgcacggggctatcaatgt-gggatacag +>canFam2.chr14(-):11090081-11090120|sequence_index=0|block_index=4|species=canFam2|canFam2_4_0 +ACATCAtgctagatcctggactatgagctg-ggtatatag +>dasNov1.scaffold_256527(+):625-665|sequence_index=0|block_index=4|species=dasNov1|dasNov1_4_0 +CCTTTGTGCTAGCCACTGGGATGAAAGCTAGGGAACACAG + +>hg17.chr7(+):127471910-127472074|sequence_index=0|block_index=5|species=hg17|hg17_5_0 +caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG +>panTro1.chr6(+):129885791-129885955|sequence_index=0|block_index=5|species=panTro1|panTro1_5_0 +caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG +>rheMac2.chr3(+):165788723-165788885|sequence_index=0|block_index=5|species=rheMac2|rheMac2_5_0 +caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G +>mm7.chr6(+):28990714-28990875|sequence_index=0|block_index=5|species=mm7|mm7_5_0 +caaaaaccaa------------------------------------------------------------------------------------------------aaaaACCTATAGC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAG +>rn3.chr4(+):56183448-56183705|sequence_index=0|block_index=5|species=rn3|rn3_5_0 +--ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG +>bosTau2.chr4(-):50243566-50243734|sequence_index=0|block_index=5|species=bosTau2|bosTau2_5_0 +atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG +>canFam2.chr14(-):11089913-11090081|sequence_index=0|block_index=5|species=canFam2|canFam2_5_0 +cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA +>dasNov1.scaffold_256527(+):665-786|sequence_index=0|block_index=5|species=dasNov1|dasNov1_5_0 +CAGTGAGCAA-----------------------------------------------------------------------------------------------CAGCCTGGCTCCGT-CC--GGGGGCCGCTCAGCAGCTC-GGGAGCGTGGAGACG---GGAAGTCTGTCACGCGATGCG-----------CTGGGCCCG------------CTGTTCCCGCCCCCCTCC---CCCC----------------TTTCCCAAG + +>hg17.chr7(+):127472074-127472258|sequence_index=0|block_index=6|species=hg17|hg17_6_0 +TTTTAAA------CATTTACCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttt-ccc-tgggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagtt +>panTro1.chr6(+):129885955-129886139|sequence_index=0|block_index=6|species=panTro1|panTro1_6_0 +TTTTAAA------CATTTACCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttt-tcc-tgggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagtt +>rheMac2.chr3(+):165788885-165789069|sequence_index=0|block_index=6|species=rheMac2|rheMac2_6_0 +TTTTAAA------CATTTACTCTCCCAGTAGCCTTGCATCTCGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTGTACGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttt-tcc-tgggcacccctgtgttcttggcactggaaaagtaccaggacttaaatagta +>mm7.chr6(+):28990875-28991025|sequence_index=0|block_index=6|species=mm7|mm7_6_0 +TTTAAAGAAAGTACCCCCTCCTTTCCAGT-GCCTCAAATCTAGAAGAATATTCATAGTGAAGT-GC------------------------ACAGCCGGGTGGTGCATGGTA-ATCTGGAAGTCACCTCTGCAAATCTT-TCC----------------TGTTGGTGCTGTGAAGGCACCAGGACTTCAAGAGTA +>rn3.chr4(+):56183705-56183879|sequence_index=0|block_index=6|species=rn3|rn3_6_0 +TTTAAAAGAAGT-CCCACTCCTTTCCAGT-GCCCTAGATCTAGAAGCACATTCATAATGATGT-ACAC-----TAACCC----------GACAGCTGTGTGGTATATGGTA-TCCCGGAAGTCACCTCAGCAAACCTT-TCCCGGGGAACCTACATGGTGTTGGTGCTGTGAAGGTACCAGGTTGTCAAGGGTA +>canFam2.chr14(-):11089743-11089913|sequence_index=0|block_index=6|species=canFam2|canFam2_6_0 +TTTTAAA------TATCTGC-TTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTC-TTC-TGAGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA----------- +>dasNov1.scaffold_256527(+):786-964|sequence_index=0|block_index=6|species=dasNov1|dasNov1_6_0 +TTTTAAA------AATTTACCTTCCCAGTGGCGGTGAATCCGGAGGAATACGGAAACTGGGGC-GCACTACCATGACACGTGTCAAA-AATCAGTTCCGTGGTCCGTGGAGGGCCTGGGGTTC------GAAAATCTTGTCC-CGAGCACCCCCGTGCGCCTGGCACCGCGACAGTGACAGGACTGAAGCGTG- + +>hg17.chr7(+):127472258-127472280|sequence_index=0|block_index=7|species=hg17|hg17_7_0 +gatggccca-atccctgtcctct- +>panTro1.chr6(+):129886139-129886161|sequence_index=0|block_index=7|species=panTro1|panTro1_7_0 +gatggccca-atccctgtcctct- +>rheMac2.chr3(+):165789069-165789091|sequence_index=0|block_index=7|species=rheMac2|rheMac2_7_0 +gatggccca-atccctgtcctct- +>mm7.chr6(+):28991025-28991048|sequence_index=0|block_index=7|species=mm7|mm7_7_0 +AATGGCAGAGGGCTCTGTTCTCT- +>rn3.chr4(+):56183879-56183902|sequence_index=0|block_index=7|species=rn3|rn3_7_0 +AATGGCAGAGGCCCCTGTTCTCT- +>canFam2.chr14(-):11089526-11089548|sequence_index=0|block_index=7|species=canFam2|canFam2_7_0 +GGAGACTTG-ATGCCTGCCTTCC- +>dasNov1.scaffold_256527(+):964-987|sequence_index=0|block_index=7|species=dasNov1|dasNov1_7_0 +GACGGCCAG-ACCTCTGCCCTCGG + +>hg17.chr7(+):127472280-127472681|sequence_index=0|block_index=8|species=hg17|hg17_8_0 +taaaacctaagggaggagaTGGAAAG-GGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATG--GAGAGGCCCTA-GTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCA------ATGTGC-AATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta--aagggccaggtagaaaacattttaggctttctaagccaagg---caaaattgaggat-attacatgggtacttatacaacaagaataaacaatt---tacacaa-ttttttgttgacagaattcaaaa---ctttat----agacac---agaaatgcaaatttcctgt +>panTro1.chr6(+):129886161-129886562|sequence_index=0|block_index=8|species=panTro1|panTro1_8_0 +taaaacctaagggaggagaTGGAAAG-GGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCA------ATGTGC-AATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta--aagggccaggtagaaaacattttaggctttctaagccaagg---caaaattgaggat-attacatgggtacttatacaacaagaataaacaatt---tacacaa-ttttttgttgacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt +>rheMac2.chr3(+):165789091-165789492|sequence_index=0|block_index=8|species=rheMac2|rheMac2_8_0 +taaaacctaatggaggagatggaATG-GGTCACCCAACCCGGACTGAGAGACAGGAATTAGCTGCAAGGGTAACCAGGACAAGCTTCTCTA---ATGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCTGGGAGAAGCGATGGATTCGTAGTTGGGCATCCCCACAGAGGGACTGGAAAGAAAAAAGACCTGGAGGAACCA------ATGTGC-AATGTATGTGTGTTTCCTGGTTcaagggctggcaaactttctcta--aagggccagatagaaaacattttaggctttgtaagccaagg---caaaatcgaggag-attacatgggtacttatacaacaagaataaacaatt---tccacaa--tttttattcacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt +>rn3.chr4(+):56183902-56184219|sequence_index=0|block_index=8|species=rn3|rn3_8_0 +------------------------------------GTCCATAGTCAAAG------------------------------AAGCCTCTCAG---ATGGAG--AGCAGGGCCTATGCAAAAGAGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTTGCAGGTTGG----------------------------CAAACAATTCCTGCTTTGCAGGCCAAGA---GGAAACTGAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAA-TTTTTGGTTGACCAAATTCAGAA---CTTTATTTGAGGATGC---TAAAGTTTAAATTTCTTTT +>canFam2.chr14(-):11089143-11089523|sequence_index=0|block_index=8|species=canFam2|canFam2_8_0 +TACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAG--AAGAGACCCCG-GTG----------------CTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTA------ACGTGC-AATGTA------TTTTCTAGTTCCAgggttggcaaactttctctct-aagggtgggatgataaacattttaggcttttcagaccaaga---ggcgacatcagag-ggtatgtaggt---------acaagagggaaaagttgcccccggaa-ttttttg--gataaaattcaaaa---ctttacttagggatgc---caaaatgtaaacttcatat +>dasNov1.scaffold_256527(+):987-1401|sequence_index=0|block_index=8|species=dasNov1|dasNov1_8_0 +CTAAATCTCGCGGAGAAGGTGGAACA-GGTTACCCAAACCCGACCGAG-GAGGCGAGTTG---GAAACGGCGACTGGGACAAGCTCCCTCA---GAGACGGAGAGAGACCCCA-GTGGAAGGGGGGAGAGGCTCTTAGGGAAACGATGGGGGGACCCGCCCGCACCCGCACAGAGGCGCTGGCAGGCACAGCGGCCCCGAGGAGCCC------AGGAGC-AGGGC-TGTGT-TCCCCTGCATcaggggttggcaaactttttctgcaaagggccagatagtaaatattttaggctttgcaaaccaagaagtagaaagggaggcc-attatgtacgtatttatatagcaagagagaacattt---cccacaatttttttattgacagaatttaaaacttctttattgatgaacaccaaagaaacttgaatttcatat + +>hg17.chr7(+):127472681-127472715|sequence_index=0|block_index=9|species=hg17|hg17_9_0 +aattttcccat---gagaactattcttcttttgtttt +>rheMac2.chr3(+):165789492-165789526|sequence_index=0|block_index=9|species=rheMac2|rheMac2_9_0 +aattttcacat---aagaactattcttcttttgtttt +>panTro1.chr6(+):129886562-129886596|sequence_index=0|block_index=9|species=panTro1|panTro1_9_0 +aattttcccgt---gagaactattcttcttttgtttt +>canFam2.chr14(-):11089108-11089143|sequence_index=0|block_index=9|species=canFam2|canFam2_9_0 +aatggtcatgt--ccataactattcttcttttatttt +>dasNov1.scaffold_256527(+):1401-1433|sequence_index=0|block_index=9|species=dasNov1|dasNov1_9_0 +aattttcacatatcacgaagtatttttttttt----- + diff -r 99dcba7af5b6 -r e929a2d803e4 test-data/maf_split_by_species_collapsed_out.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_split_by_species_collapsed_out.maf Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,61 @@ +##maf version=1 +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG + diff -r 99dcba7af5b6 -r e929a2d803e4 test-data/maf_split_by_species_in.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_split_by_species_in.maf Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,11 @@ +##maf version=1 +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + diff -r 99dcba7af5b6 -r e929a2d803e4 test-data/maf_split_by_species_not_collapsed_out.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_split_by_species_not_collapsed_out.maf Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,61 @@ +##maf version=1 +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +a score=2047408.0 +s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG +s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG +s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + diff -r 99dcba7af5b6 -r e929a2d803e4 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 04 10:31:23 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 04 10:40:16 2009 -0400 @@ -90,6 +90,7 @@ <section name="Fetch Alignments" id="fetchAlign"> <tool file="maf/interval2maf_pairwise.xml" /> <tool file="maf/interval2maf.xml" /> + <tool file="maf/maf_split_by_species.xml"/> <tool file="maf/interval_maf_to_merged_fasta.xml" /> <tool file="maf/genebed_maf_to_fasta.xml"/> <tool file="maf/maf_stats.xml"/> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/annotation_profiler/annotation_profiler_for_interval.py --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:40:16 2009 -0400 @@ -22,10 +22,12 @@ fmt_size = struct.calcsize( fmt ) def __init__( self, filename ): self.file_size = os.stat( filename ).st_size - self.file = open( filename, 'rb' ) + self.file = open( filename, 'rb' ) + self.filename = filename self.length = int( self.file_size / self.fmt_size / 2 ) self._cached_ranges = [ None for i in xrange( self.length ) ] def __getitem__( self, i ): + old_i = i if self._cached_ranges[i] is not None: return self._cached_ranges[i] if i < 0: i = self.length + i @@ -35,7 +37,13 @@ start = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] end = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] except Exception, e: - raise IndexError, e + print 'filename', self.filename + print 'len', len( self ) + print 'fmtsize', self.fmt_size + print 'index', i + print 'old i', old_i + print 'offset', offset + raise IndexError( str( e ) ) self._cached_ranges[i] = ( start, end ) return start, end def __len__( self ): @@ -141,20 +149,24 @@ self.chromosome_coverage[chrom] = bx.bitset.BitSet( chrom_length ) self.chromosome_coverage[chrom].set_range( region_start, region_length ) - for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): - if table_name not in self.table_coverage: - self.table_coverage[table_name] = 0 - self.table_chromosome_size[table_name] = {} - self.table_regions_overlaped_count[table_name] = 0 - self.interval_table_overlap_count[table_name] = 0 - self.table_chromosome_count[table_name] = {} - if chrom not in self.table_chromosome_size[table_name]: - self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage - self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) - self.table_coverage[table_name] += coverage - if coverage: - self.interval_table_overlap_count[table_name] += 1 - self.table_regions_overlaped_count[table_name] += regions + try: + for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): + if table_name not in self.table_coverage: + self.table_coverage[table_name] = 0 + self.table_chromosome_size[table_name] = {} + self.table_regions_overlaped_count[table_name] = 0 + self.interval_table_overlap_count[table_name] = 0 + self.table_chromosome_count[table_name] = {} + if chrom not in self.table_chromosome_size[table_name]: + self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage + self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) + self.table_coverage[table_name] += coverage + if coverage: + self.interval_table_overlap_count[table_name] += 1 + self.table_regions_overlaped_count[table_name] += regions + except Exception, e: + print "chrom:%s, start:%s, end%s:." % ( chrom, start, end ) + raise e def iter_table_coverage( self ): def get_nr_coverage(): #returns non-redundant coverage, where user's input intervals have been collapse to resolve overlaps diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/genebed_maf_to_fasta.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,8 +1,8 @@ -<tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks"> +<tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1"> <description>given a set of coding exon intervals</description> <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#end if +#end if# --overwrite_with_gaps=$overwrite_with_gaps </command> <inputs> <param name="input1" type="data" format="bed" label="Gene BED File"> @@ -29,42 +29,48 @@ <when value="cached"> <param name="maf_identifier" type="select" label="MAF Type" > <options from_file="maf_index.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - <column name="dbkey" index="2"/> - <column name="species" index="3"/> - <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> - <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> + <column name="name" index="0"/> + <column name="value" index="1"/> + <column name="dbkey" index="2"/> + <column name="species" index="3"/> + <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> + <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> </options> </param> <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> <options from_file="maf_index.loc"> - <column name="uid" index="1"/> - <column name="value" index="3"/> - <column name="name" index="3"/> - <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> - <filter type="multiple_splitter" column="3" separator=","/> + <column name="uid" index="1"/> + <column name="value" index="3"/> + <column name="name" index="3"/> + <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> + <filter type="multiple_splitter" column="3" separator=","/> </options> </param> </when> </conditional> - </inputs> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <option value="True" selected="true">No</option> + <option value="False">Yes</option> + </param> + </inputs> <outputs> <data format="fasta" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="8.bed"/> - <param name="maf_source" value="cached"/> + <param name="maf_source" value="cached"/>in aligning species <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_out.fasta" /> </test> <test> <param name="input1" value="8.bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="4.maf"/> - <param name="species" value="hg17,panTro1"/> + <param name="species" value="hg17,panTro1"/> + <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_user_out.fasta" /> </test> </tests> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/interval2maf.py --- a/tools/maf/interval2maf.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/interval2maf.py Fri Sep 04 10:40:16 2009 -0400 @@ -20,6 +20,8 @@ -i, --interval_file=i: Input interval file -o, --output_file=o: Output MAF file -p, --species=p: Species to include in output + -P, --split_blocks_by_species=P: Split blocks by species + -r, --remove_all_gap_columns=r: Remove all Gap columns -l, --indexLocation=l: Override default maf_index.loc file -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc ) """ @@ -45,25 +47,21 @@ if options.dbkey: dbkey = options.dbkey else: dbkey = None if dbkey in [None, "?"]: - print >>sys.stderr, "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." - sys.exit() + maf_utilities.tool_fail( "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." ) species = maf_utilities.parse_species_option( options.species ) if options.chromCol: chromCol = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() + maf_utilities.tool_fail( "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." ) if options.startCol: startCol = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() + maf_utilities.tool_fail( "Start column not set, click the pencil icon in the history item to set the metadata attributes." ) if options.endCol: endCol = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() + maf_utilities.tool_fail( "End column not set, click the pencil icon in the history item to set the metadata attributes." ) if options.strandCol: strandCol = int( options.strandCol ) - 1 else: @@ -71,13 +69,17 @@ if options.interval_file: interval_file = options.interval_file else: - print >>sys.stderr, "Input interval file has not been specified." - sys.exit() + maf_utilities.tool_fail( "Input interval file has not been specified." ) if options.output_file: output_file = options.output_file else: - print >>sys.stderr, "Output file has not been specified." - sys.exit() + maf_utilities.tool_fail( "Output file has not been specified." ) + + split_blocks_by_species = remove_all_gap_columns = False + if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species': + split_blocks_by_species = True + if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns': + remove_all_gap_columns = True #Finish parsing command line #Open indexed access to MAFs @@ -87,16 +89,13 @@ else: index = maf_utilities.maf_index_by_uid( options.mafType, options.mafIndexFile ) if index is None: - print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( options.mafType ) - sys.exit() + maf_utilities.tool_fail( "The MAF source specified (%s) appears to be invalid." % ( options.mafType ) ) elif options.mafFile: index, index_filename = maf_utilities.open_or_build_maf_index( options.mafFile, options.mafIndex, species = [dbkey] ) if index is None: - print >> sys.stderr, "Your MAF file appears to be malformed." - sys.exit() + maf_utilities.tool_fail( "Your MAF file appears to be malformed." ) else: - print >>sys.stderr, "Desired source MAF type has not been specified." - sys.exit() + maf_utilities.tool_fail( "Desired source MAF type has not been specified." ) #Create MAF writter out = bx.align.maf.Writer( open(output_file, "w") ) @@ -105,10 +104,20 @@ num_blocks = 0 num_regions = None for num_regions, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( interval_file, 'r' ), chrom_col = chromCol, start_col = startCol, end_col = endCol, strand_col = strandCol, fix_strand = True, return_header = False, return_comments = False ) ): - src = "%s.%s" % ( dbkey, region.chrom ) - for block in maf_utilities.get_chopped_blocks_for_region( index, src, region, species, mincols ): - out.write( block ) - num_blocks += 1 + src = maf_utilities.src_merge( dbkey, region.chrom ) + for block in index.get_as_iterator( src, region.start, region.end ): + if split_blocks_by_species: + blocks = [ new_block for new_block in maf_utilities.iter_blocks_split_by_species( block ) if maf_utilities.component_overlaps_region( new_block.get_component_by_src_start( dbkey ), region ) ] + else: + blocks = [ block ] + for block in blocks: + block = maf_utilities.chop_block_by_region( block, src, region ) + if block is not None: + block = maf_utilities.orient_block_by_region( block, src, region ) + if remove_all_gap_columns: + block.remove_all_gap_columns() + out.write( block ) + num_blocks += 1 #Close output MAF out.close() diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/interval2maf.xml Fri Sep 04 10:40:16 2009 -0400 @@ -3,6 +3,9 @@ <command interpreter="python"> #if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #else:#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species + #end if + --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species + #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species":# --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns #end if </command> <inputs> @@ -48,7 +51,22 @@ </options> </param> </when> - </conditional> + </conditional> + <conditional name="split_blocks_by_species_selector"> + <param name="split_blocks_by_species" type="select" label="Split blocks by species" help="See the Split MAF blocks by Species tool for more information."> + <option value="split_blocks_by_species">Split by species</option> + <option value="dont_split_blocks_by_species" selected="true">Do not split</option> + </param> + <when value="dont_split_blocks_by_species"> +  + </when> + <when value="split_blocks_by_species"> + <param name="remove_all_gap_columns" type="select" label="Collapse empty alignment columns"> + <option value="remove_all_gap_columns" selected="true">Collapse empty columns</option> + <option value="do_not_remove_all_gap_columns">Do not collapse</option> + </param> + </when> + </conditional> </inputs> <outputs> <data format="maf" name="out_file1"/> @@ -59,6 +77,7 @@ <param name="maf_source" value="cached"/> <param name="mafType" value="ENCODE_TBA_hg17"/> <param name="species" value="hg17,panTro1,baboon,marmoset,galago,rn3,mm6,rabbit,cow,canFam1,rfbat,shrew,armadillo,tenrec,monDom1,tetNig1,fr1,rheMac1,galGal2,xenTro1,danRer2,elephant,platypus,hedgehog,colobus_monkey,dusky_titi,owl_monkey,mouse_lemur"/> + <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> <output name="out_file1" file="fsa_interval2maf.dat" /> </test> <test> @@ -66,6 +85,7 @@ <param name="maf_source" value="user"/> <param name="mafFile" value="fsa_interval2maf.dat"/> <param name="species" value="hg17,panTro1,baboon,marmoset,galago,rn3,mm6,rabbit,cow,canFam1,rfbat,shrew,armadillo,tenrec,monDom1,tetNig1,fr1,rheMac1,galGal2,xenTro1,danRer2,elephant,platypus,hedgehog,colobus_monkey,dusky_titi,owl_monkey,mouse_lemur"/> + <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> <output name="out_file1" file="fsa_interval2maf.dat" /> </test> </tests> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/interval2maf_pairwise.xml --- a/tools/maf/interval2maf_pairwise.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/interval2maf_pairwise.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks"> +<tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks" version="1.0.1"> <description>given a set of genomic intervals</description> <command interpreter="python">interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command> <inputs> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/interval_maf_to_merged_fasta.py --- a/tools/maf/interval_maf_to_merged_fasta.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.py Fri Sep 04 10:40:16 2009 -0400 @@ -19,6 +19,7 @@ -i, --interval_file=i: Input interval file -o, --output_file=o: Output MAF file -p, --species=p: Species to include in output + -O, --overwrite_with_gaps=O: Overwrite bases found in a lower-scoring block with gaps interior to the sequence for a species. -z, --mafIndexFileDir=z: Directory of local maf_index.loc file usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR @@ -93,6 +94,11 @@ strand_col = int( options.strandCol ) - 1 mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir + + overwrite_with_gaps = True + if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == 'false': + overwrite_with_gaps = False + #Finish parsing command line #get index for mafs based on type @@ -127,7 +133,7 @@ try: starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed( line ) #create spliced alignment object - alignment = maf_utilities.get_spliced_region_alignment( index, primary_species, fields[0], starts, ends, strand = '+', species = species, mincols = mincols ) + alignment = maf_utilities.get_spliced_region_alignment( index, primary_species, fields[0], starts, ends, strand = '+', species = species, mincols = mincols, overwrite_with_gaps = overwrite_with_gaps ) primary_name = secondary_name = fields[3] alignment_strand = fields[5] except Exception, e: @@ -136,7 +142,7 @@ else: #Process as standard intervals try: #create spliced alignment object - alignment = maf_utilities.get_region_alignment( index, primary_species, line.chrom, line.start, line.end, strand = '+', species = species, mincols = mincols ) + alignment = maf_utilities.get_region_alignment( index, primary_species, line.chrom, line.start, line.end, strand = '+', species = species, mincols = mincols, overwrite_with_gaps = overwrite_with_gaps ) primary_name = "%s(%s):%s-%s" % ( line.chrom, line.strand, line.start, line.end ) secondary_name = "" alignment_strand = line.strand diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,8 +1,8 @@ -<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks"> +<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"> <description>given a set of genomic intervals</description> <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} -#end if +#end if# --overwrite_with_gaps=$overwrite_with_gaps </command> <inputs> <page> @@ -30,25 +30,29 @@ <when value="cached"> <param name="maf_identifier" type="select" label="MAF Type" > <options from_file="maf_index.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - <column name="dbkey" index="2"/> - <column name="species" index="3"/> - <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> - <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> + <column name="name" index="0"/> + <column name="value" index="1"/> + <column name="dbkey" index="2"/> + <column name="species" index="3"/> + <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> + <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> </options> </param> <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> <options from_file="maf_index.loc"> - <column name="uid" index="1"/> - <column name="value" index="3"/> - <column name="name" index="3"/> - <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> - <filter type="multiple_splitter" column="3" separator=","/> + <column name="uid" index="1"/> + <column name="value" index="3"/> + <column name="name" index="3"/> + <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> + <filter type="multiple_splitter" column="3" separator=","/> </options> </param> </when> </conditional> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <option value="True" selected="true">No</option> + <option value="False">Yes</option> + </param> </page> </inputs> <outputs> @@ -59,21 +63,24 @@ <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> - <param name="species" value="hg18,mm8"/> + <param name="species" value="hg18,mm8"/> + <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> </test> <test> <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" /> </test> <test> <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="5.maf"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" /> </test> </tests> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_filter.py --- a/tools/maf/maf_filter.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_filter.py Fri Sep 04 10:40:16 2009 -0400 @@ -46,7 +46,7 @@ i = 0 blocks_kept = 0 for i, maf_block in enumerate( maf_reader ): - if min_size <= maf_block.components[0].size <= max_size: + if min_size <= maf_block.text_size <= max_size: local = {'maf_block':maf_block, 'ret_val':False} execfile( script_file, {}, local ) if local['ret_val']: diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_limit_size.py --- a/tools/maf/maf_limit_size.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_limit_size.py Fri Sep 04 10:40:16 2009 -0400 @@ -28,7 +28,7 @@ blocks_kept = 0 i = 0 for i, m in enumerate( maf_reader ): - if min_size <= m.components[0].size <= max_size: + if min_size <= m.text_size <= max_size: maf_writer.write( m ) blocks_kept += 1 print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 ) diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_limit_size.xml --- a/tools/maf/maf_limit_size.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_limit_size.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="maf_limit_size1" name="Filter MAF blocks"> +<tool id="maf_limit_size1" name="Filter MAF blocks" version="1.0.1"> <description>by Size</description> <command interpreter="python">maf_limit_size.py $input1 $out_file1 $min_size $max_size</command> <inputs> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_limit_to_species.py --- a/tools/maf/maf_limit_to_species.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_limit_to_species.py Fri Sep 04 10:40:16 2009 -0400 @@ -11,13 +11,18 @@ from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) import bx.align.maf +from galaxy.tools.util import maf_utilities import sys assert sys.version_info[:2] >= ( 2, 4 ) def main(): - species = sys.argv[1].split( ',' ) + species = maf_utilities.parse_species_option( sys.argv[1] ) + if species: + spec_len = len( species ) + else: + spec_len = 0 try: maf_reader = bx.align.maf.Reader( open( sys.argv[2],'r' ) ) maf_writer = bx.align.maf.Writer( open( sys.argv[3],'w' ) ) @@ -30,10 +35,11 @@ maf_blocks_kept = 0 for m in maf_reader: - if species != ['None']: + if species: m = m.limit_to_species( species ) m.remove_all_gap_columns() - if ( species == ['None'] or allow_partial or len( m.components ) == len( species ) ) and len( m.components ) > min_species_per_block: + spec_in_block_len = len( maf_utilities.get_species_in_block( m ) ) + if ( not species or allow_partial or spec_in_block_len == spec_len ) and spec_in_block_len > min_species_per_block: maf_writer.write( m ) maf_blocks_kept += 1 diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_split_by_species.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/maf_split_by_species.py Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,44 @@ +#!/usr/bin/env python + +""" +Read a maf and split blocks by unique species combinations +""" +import sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.align import maf +from galaxy.tools.util import maf_utilities +from galaxy.util import string_as_bool + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + try: + maf_reader = maf.Reader( open( sys.argv[1] ) ) + except Exception, e: + maf_utilities.tool_fail( "Error opening MAF: %s" % e ) + try: + out = maf.Writer( open( sys.argv[2], "w") ) + except Exception, e: + maf_utilities.tool_fail( "Error opening file for output: %s" % e ) + try: + collapse_columns = string_as_bool( sys.argv[3] ) + except Exception, e: + maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e ) + + start_count = 0 + end_count = 0 + for start_count, start_block in enumerate( maf_reader ): + for block in maf_utilities.iter_blocks_split_by_species( start_block ): + if collapse_columns: + block.remove_all_gap_columns() + out.write( block ) + end_count += 1 + out.close() + + if end_count: + print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 ) + else: + print "No alignment blocks were created." + +if __name__ == "__main__": __main__() diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_split_by_species.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/maf_split_by_species.xml Fri Sep 04 10:40:16 2009 -0400 @@ -0,0 +1,216 @@ +<tool id="MAF_split_blocks_by_species1" name="Split MAF blocks" version="1.0.0"> + <description>by Species</description> + <command interpreter="python">maf_split_by_species.py $input1 $out_file1 $collapse_columns</command> + <inputs> + <param format="maf" name="input1" type="data" label="MAF file to split"/> + <param name="collapse_columns" type="select" label="Collapse empty alignment columns" help="Removes columns that are gaps in all sequences"> + <option value="True" selected="true">Yes</option> + <option value="False">No</option> + </param> + </inputs> + <outputs> + <data format="maf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="maf_split_by_species_in.maf"/> + <param name="collapse_columns" value="True"/> + <output name="out_file1" file="maf_split_by_species_collapsed_out.maf"/> + </test> + <test> + <param name="input1" value="maf_split_by_species_in.maf"/> + <param name="collapse_columns" value="False"/> + <output name="out_file1" file="maf_split_by_species_not_collapsed_out.maf"/> + </test> + </tests> + <help> + +**What it does** + +This tool examines each MAF block for multiple occurrences of a species in a single block. When this occurs, a block is split into multiple blocks where every combination of one sequence per species per block is represented. + +The interface for this tool has two inputs: + + * **MAF file to split**. Choose multiple alignments from history to be split by species. + * **Collapse empty alignment columns**. Should alignment columns containing only gaps in the new blocks be removed. + +----- + +**Example 1**: **Collapse empty alignment columns is Yes**: + +For the following alignment:: + + ##maf version=1 + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +the tool will create **a single** history item containing 12 alignment blocks (notice that no columns contain only gaps):: + + ##maf version=1 + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG + +----- + +**Example 1**: **Collapse empty alignment columns is Yes**: + +For the following alignment:: + + ##maf version=1 + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +the tool will create **a single** history item containing 12 alignment blocks (notice that some columns contain only gaps):: + + ##maf version=1 + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + + a score=2047408.0 + s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG + s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG + s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG + +------- + +.. class:: infomark + +**About formats** + +**MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes. + + - The .maf format is line-oriented. Each multiple alignment ends with a blank line. + - Each sequence in an alignment is on a single line. + - Lines starting with # are considered to be comments. + - Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment. + - Some MAF files may contain two optional line types: + + - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; + - An "e" line containing information about the size of the gap between the alignments that span the current block. + + </help> +</tool> + diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_stats.py --- a/tools/maf/maf_stats.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_stats.py Fri Sep 04 10:40:16 2009 -0400 @@ -64,16 +64,19 @@ total_length += region_length coverage = { dbkey: BitSet( region_length ) } - for block in maf_utilities.get_chopped_blocks_for_region( index, src, region, force_strand='+' ): - #make sure all species are known - for c in block.components: - spec = c.src.split( '.' )[0] + + for block in index.get_as_iterator( src, region.start, region.end ): + for spec in maf_utilities.get_species_in_block( block ): if spec not in coverage: coverage[spec] = BitSet( region_length ) - start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start ) - for i in range( len( alignment[dbkey] ) ): - for spec, text in alignment.items(): - if text[i] != '-': - coverage[spec].set( start_offset + i ) + for block in maf_utilities.iter_blocks_split_by_species( block ): + if maf_utilities.component_overlaps_region( block.get_component_by_src( src ), region ): + #need to chop and orient the block + block = maf_utilities.orient_block_by_region( maf_utilities.chop_block_by_region( block, src, region ), src, region, force_strand = '+' ) + start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start ) + for i in range( len( alignment[dbkey] ) ): + for spec, text in alignment.items(): + if text[i] != '-': + coverage[spec].set( start_offset + i ) if summary: #record summary for key in coverage.keys(): diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_stats.xml --- a/tools/maf/maf_stats.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_stats.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="maf_stats1" name="MAF Coverage Stats"> +<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"> <description>Alignment coverage information</description> <command interpreter="python"> maf_stats.py diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_to_fasta.xml Fri Sep 04 10:40:16 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="MAF_To_Fasta1" name="Maf to FASTA"> +<tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1"> <description>Converts a MAF formated file to FASTA format</description> <command interpreter="python"> #if $fasta_target_type.fasta_type == "multiple":#maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks @@ -47,7 +47,7 @@ <param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/> <param name="complete_blocks" value="partial_allowed"/> <param name="fasta_type" value="multiple"/> - <output name="out_file1" file="cf_maf2fasta.dat" ftype="fasta"/> + <output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/> </test> </tests> <help> diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_to_fasta_concat.py --- a/tools/maf/maf_to_fasta_concat.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_to_fasta_concat.py Fri Sep 04 10:40:16 2009 -0400 @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -Read a maf and print the text as a fasta file, concatenating blocks +Read a maf and output a single block fasta file, concatenating blocks usage %prog species1,species2 maf_file out_file """ @@ -15,28 +15,43 @@ assert sys.version_info[:2] >= ( 2, 4 ) def __main__(): - print "Restricted to species:", sys.argv[1] + try: + species = maf_utilities.parse_species_option( sys.argv[1] ) + except Exception, e: + maf_utilities.tool_fail( "Error determining species value: %s" % e ) + try: + input_filename = sys.argv[2] + except Exception, e: + maf_utilities.tool_fail( "Error reading MAF filename: %s" % e ) + try: + file_out = open( sys.argv[3], 'w' ) + except Exception, e: + maf_utilities.tool_fail( "Error opening file for output: %s" % e ) - texts = {} + if species: + print "Restricted to species: %s" % ', '.join( species ) + else: + print "Not restricted to species." - input_filename = sys.argv[2] - output_filename = sys.argv[3] - species = sys.argv[1].split( ',' ) + if not species: + try: + species = maf_utilities.get_species_in_maf( input_filename ) + except Exception, e: + maf_utilities.tool_fail( "Error determining species in input MAF: %s" % e ) - if "None" in species: - species = maf_utilities.get_species_in_maf( input_filename ) - - file_out = open( output_filename, 'w' ) for spec in species: file_out.write( ">" + spec + "\n" ) try: - for block in maf.Reader( open( input_filename, 'r' ) ): - component = block.get_component_by_src_start( spec ) - if component: file_out.write( component.text ) - else: file_out.write( "-" * block.text_size ) - except: - print >>sys.stderr, "Your MAF file appears to be malformed." - sys.exit() + for start_block in maf.Reader( open( input_filename, 'r' ) ): + for block in maf_utilities.iter_blocks_split_by_species( start_block ): + block.remove_all_gap_columns() #remove extra gaps + component = block.get_component_by_src_start( spec ) #blocks only have one occurrence of a particular species, so this is safe + if component: + file_out.write( component.text ) + else: + file_out.write( "-" * block.text_size ) + except Exception, e: + maf_utilities.tool_fail( "Your MAF file appears to be malformed: %s" % e ) file_out.write( "\n" ) file_out.close() diff -r 99dcba7af5b6 -r e929a2d803e4 tools/maf/maf_to_fasta_multiple_sets.py --- a/tools/maf/maf_to_fasta_multiple_sets.py Fri Sep 04 10:31:23 2009 -0400 +++ b/tools/maf/maf_to_fasta_multiple_sets.py Fri Sep 04 10:40:16 2009 -0400 @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -Read a maf and print the text as a fasta file. +Read a maf and output a multiple block fasta file. """ #Dan Blankenberg import sys @@ -13,35 +13,46 @@ assert sys.version_info[:2] >= ( 2, 4 ) def __main__(): - print "Restricted to species:", sys.argv[3] + try: + maf_reader = maf.Reader( open( sys.argv[1] ) ) + except Exception, e: + maf_utilities.tool_fail( "Error opening input MAF: %s" % e ) + try: + file_out = open( sys.argv[2], 'w' ) + except Exception, e: + maf_utilities.tool_fail( "Error opening file for output: %s" % e ) + try: + species = maf_utilities.parse_species_option( sys.argv[3] ) + if species: + num_species = len( species ) + else: + num_species = 0 + except Exception, e: + maf_utilities.tool_fail( "Error determining species value: %s" % e ) + try: + partial = sys.argv[4] + except Exception, e: + maf_utilities.tool_fail( "Error determining keep partial value: %s" % e ) - input_filename = sys.argv[1] - output_filename = sys.argv[2] - species = sys.argv[3].split( ',' ) - partial = sys.argv[4] - num_species = len( species ) + if species: + print "Restricted to species: %s" % ', '.join( species ) + else: + print "Not restricted to species." - file_in = open( input_filename, 'r' ) - try: - maf_reader = maf.Reader( file_in ) - - file_out = open( output_filename, 'w' ) - - for block_num, block in enumerate( maf_reader ): - if "None" not in species: - block = block.limit_to_species( species ) - if len( block.components ) < num_species and partial == "partial_disallowed": continue - for component in block.components: - spec, chrom = maf.src_split( component.src ) - if not spec or not chrom: - spec = chrom = component.src - file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, suffix = "%s_%i" % ( spec, block_num ) ) ) - file_out.write( "%s\n" % component.text ) - file_out.write( "\n" ) - file_in.close() - except Exception, e: - print >>sys.stderr, "Your MAF file appears to be malformed:", e - sys.exit() + for block_num, block in enumerate( maf_reader ): + if species: + block = block.limit_to_species( species ) + if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue + spec_counts = {} + for component in block.components: + spec, chrom = maf_utilities.src_split( component.src ) + if spec not in spec_counts: + spec_counts[ spec ] = 0 + else: + spec_counts[ spec ] += 1 + file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) ) + file_out.write( "%s\n" % component.text ) + file_out.write( "\n" ) file_out.close() if __name__ == "__main__": __main__()

1 0

[hg] galaxy 2659: Added a new option to 'fetch closest features'...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ba2412c2a4d9 changeset: 2659:ba2412c2a4d9 user: guru date: Wed Sep 02 13:36:16 2009 -0400 description: Added a new option to 'fetch closest features' tool to return the closest feature either upstream or downstream. 3 file(s) affected in this change: test-data/closest_features_either.interval tools/new_operations/flanking_features.py tools/new_operations/flanking_features.xml diffs (524 lines): diff -r 0cb12b9d9d4d -r ba2412c2a4d9 test-data/closest_features_either.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_features_either.interval Wed Sep 02 13:36:16 2009 -0400 @@ -0,0 +1,424 @@ +chr22 30128507 30133507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30132507 30137507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30140507 30145507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 30128507 30133507 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uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31740507 31745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31732507 31737507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31744507 31749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31736507 31741507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31748507 31753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31740507 31745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31752507 31757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31744507 31749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31756507 31761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31748507 31753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31760507 31765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31752507 31757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31764507 31769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31756507 31761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31768507 31773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31760507 31765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31772507 31777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31764507 31769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31776507 31781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31768507 31773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31780507 31785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31772507 31777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31784507 31789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31776507 31781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31788507 31793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31780507 31785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31792507 31797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31784507 31789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31796507 31801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31788507 31793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31800507 31805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31792507 31797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31804507 31809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31796507 31801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31808507 31813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31800507 31805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31812507 31817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31804507 31809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31816507 31821507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31808507 31813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31820507 31825507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + chr22 31812507 31817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Tue Sep 01 17:01:44 2009 -0400 +++ b/tools/new_operations/flanking_features.py Wed Sep 02 13:36:16 2009 -0400 @@ -62,12 +62,16 @@ def proximal_region_finder(readers, region, comments=True): primary = readers[0] features = readers[1] + either = False if region == 'Upstream': up, down = True, False elif region == 'Downstream': up, down = False, True else: up, down = True, True + if region == 'Either': + either = True + # Read features into memory: rightTree = quicksect.IntervalTree() for item in features: @@ -107,14 +111,29 @@ res_ind = ends.index(max(ends)) #fetch the index of the closest interval i.e. the interval with the max end from the results_up list else: res_ind = 0 - map(outfields.append, result_up[res_ind].other) - yield outfields + if not(either): + map(outfields.append, result_up[res_ind].other) + yield outfields if result_down: outfields = list(interval) - map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + if not(either): + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + yield outfields + + if either: + if result_up and result_down: + if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)): + map(outfields.append, result_up[res_ind].other) + else: + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval + elif result_up: + map(outfields.append, result_up[res_ind].other) + else: + map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields - + + def main(): options, args = doc_optparse.parse( __doc__ ) try: diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.xml --- a/tools/new_operations/flanking_features.xml Tue Sep 01 17:01:44 2009 -0400 +++ b/tools/new_operations/flanking_features.xml Wed Sep 02 13:36:16 2009 -0400 @@ -1,10 +1,11 @@ -<tool id="flanking_features_1" name="Fetch closest feature" version="2.0.0"> +<tool id="flanking_features_1" name="Fetch closest feature" version="3.0.0"> <description> for every interval</description> <command interpreter="python">flanking_features.py $input1 $input2 $out_file1 $direction -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command> <inputs> <param format="interval" name="input1" type="data" label="For every interval in"/> - <param format="interval" name="input2" type="data" label="Fetch features from"/> - <param name="direction" type="select" label="Location of the flanking features"> + <param format="interval" name="input2" type="data" label="Fetch closest feature(s) from"/> + <param name="direction" type="select" label="Located"> + <option value="Either">Either Upstream or Downstream</option> <option value="Both">Both Upstream and Downstream</option> <option value="Upstream">Upstream</option> <option value="Downstream">Downstream</option> @@ -14,13 +15,19 @@ <data format="interval" name="out_file1" /> </outputs> <tests> - <test> - <param name="input1" value="4_windows.bed"/> + <test> + <param name="input1" value="4_windows.bed"/> + <param name="input2" value="4_windows_2.bed"/> + <param name="direction" value="Either"/> + <output name="out_file1" file="closest_features_either.interval"/> + </test> + <test> + <param name="input1" value="4_windows.bed"/> <param name="input2" value="4_windows_2.bed"/> <param name="direction" value="Both"/> <output name="out_file1" file="closest_features.interval"/> - </test> - <test> + </test> + <test> <param name="input1" value="4_windows.bed"/> <param name="input2" value="4_windows_2.bed"/> <param name="direction" value="Upstream"/>

1 0

[hg] galaxy 2660: Added pileup parser. Pardon the perl = used to...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/adff03258b45 changeset: 2660:adff03258b45 user: anton(a)nekrut-mbp.bx.psu.edu date: Fri Sep 04 10:23:37 2009 -0400 description: Added pileup parser. Pardon the perl = used to its regexes too much 12 file(s) affected in this change: static/images/pileup_parser_help1.png static/images/pileup_parser_help2.png test-data/pileup_parser.10col.20-3-yes-yes.pileup.out test-data/pileup_parser.10col.pileup test-data/pileup_parser.6col.20-3-no-no.pileup.out test-data/pileup_parser.6col.20-3-yes-no.pileup.out test-data/pileup_parser.6col.20-3-yes-yes.pileup.out test-data/pileup_parser.6col.40-3-yes-yes.pileup.out test-data/pileup_parser.6col.pileup tool_conf.xml.sample tools/samtools/pileup_parser.pl tools/samtools/pileup_parser.xml diffs (truncated from 3114 to 3000 lines): diff -r ba2412c2a4d9 -r adff03258b45 static/images/pileup_parser_help1.png Binary file static/images/pileup_parser_help1.png has changed diff -r ba2412c2a4d9 -r adff03258b45 static/images/pileup_parser_help2.png Binary file static/images/pileup_parser_help2.png has changed diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,86 @@ +chrM 13 14 A A 56 0 25 18 .......G.........^:. 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IIIIIIIIIIII:IIIII%II5IIIIIIIIII?0B1I<IIGI)II1IDII*IIIIIIII)&III&I4>%5*II4(I 1 0 0 0 62 +chrM 951 952 A A 223 0 24 81 c.,,,,,,,,,,,,,,,c,,.,,,.,,,,,,,,,,,,,,,.,..,.,..,........,,,.,,.,,,,,..,,.^:.^:.^:.^:,^:,^:, IBIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIII8IIIIIIIIIIIIIIIIIIIIICIIII4IGIIIIIIIIIIIIII? 0 2 0 0 80 +chrM 952 953 C C 179 0 24 86 ,.,,,,,,,,,,,,,,,,,,.n,,.,,a,,,,,,a,,,,,.,..,.,..,........a,,.,,.,,,,,..,a....,,a^:.^!.^!.^:a^:a IIIIIIIIIIIIIIIIIIIII"IIIII)III6I1)I4II(I7II?I9II(IIIIIIII+1III0I+214%II79IIIIBB0III%I 2 0 0 0 69 +chrM 956 957 T T 237 0 23 110 ,.,,,,,,,,,,,,,,,,,,N,,,N,,,,,,,,,,,,,,,G,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,NN,^:.^:,^:,^:,^:.^:.^:. I/IIIIIIIIIIIIIIIIII"III"III4IIIII)I6GHI63II86III0IIIIIIII8BII6+II56I.II71IIII;/+IIIDDIIIIIIIIII;II,""2I@03III 0 0 1 0 92 +chrM 957 958 C C 251 0 23 117 ,.,,,t,t,,,,,,,,,,,,.,,,.,,,,,,,,,,,,,,,.,..,.,..,........,,,.,,.,,,,,..,a....,a,...,,.......,..,..,..,.,,,...^:,^:,^:.^!.^:,^:,^:, I9III(I&IIIIIIIIIIIIIIIIIIIIIIIIII>I3III*III3IIII:IIIIIIII(/IIIBIII(&$IIIIIIII<+%III>@IIIIIIIIIIIII,II,I%(6IIII1II(-/ 1 0 0 0 97 +chrM 966 967 A A 246 0 23 125 ,$c,G,,,.,,,,,,,,,,,,,n,.,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,..,.,,,...,,..,,,......g...,,,.,,,,,,,.,.^:, I5I#IIIIIIIIIIIIIIIBI"IIIIII;IIIIIIIIIIII;2IIIIIIIIIIIII@IIIIIIIIIIIIIIIIIII6IIIIIIIIIIIIIIIIIIIIIIIIII/II#IIIIIIIIIIIII>IIII 0 1 0 0 120 +chrM 974 975 C C 255 0 23 125 ,,,,,,,.,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,..,.,,,...,,..,,,......,...,,n.,,aa,,,N,.,.,,.gg,,,,....^:n^:, IIIIIII4IIIIIIEII/I?IIIIIIII7II<IIIIIIIIIIEIIIIIIIIIIII2IIIIIIIIIIIIIIGIIIIIIIIIIIIIIII%II3IIIII"III%IIII"IIII@.IB*BIDIIIII", 1 0 1 0 113 +chrM 980 981 C C 247 0 23 123 .$.$,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,..,.,,,...,,..,,,......,...,,,.,,a,,,,.,.,.,,.gt,,,,....,,,..,.,,,,^:.^:,^:, IIIII6IIIIIIII;IIAIIIIIIIIICI5III&IIIIIII<IIIEIIIIIIIIIIIIII=IIIIIIIIII5I&IIIIIIHIIIII'III9IIIII92I6#9II3IIIIII+II>I&71'I45 0 0 1 0 112 +chrM 981 982 C C 255 0 23 122 ,$.$.$......,,,.,,.,,,,,..,,....,,,...,,.......,..,..,..,.,,,...,,..,,,......,...,,,.,,,,,,a.,.,.,,.g,,,,,....a,,..,.,,,a.,,^!, IIFBIEIIIIII?II@IIIIIIIIIIIIIII6II9IIIIIIIIIIIIIIIIIIIIIII5IIIIIIIIIIII&IIIFIIDIIII0$III<IIIII2II%9,?&IIIIII*/II+I59I)I1-) 2 0 0 0 108 +chrM 982 983 C C 252 0 23 122 .$.$.$...,,,.,,.,,,,,..,,....,,,...,,.......,..,..,..,.,,,...,,..,,,......,...,,,.,,,,,,a.,.,.,a.,,,,,,....,,,..,.a,,a.,,,^!,^!,^!, :IIIIIIIICIIIIIIIIIIIIIIIIIIIIIIIIIIAIIIIIIIIIBIIII?III2I5IIIIIIIIAI#IIIIIIIIIII&)IIIIIIIIII+II&9F8IIIIIII2II)I')I$I++)I(+ 1 0 0 0 106 +chrM 983 984 A A 250 0 23 119 .$.$.$,$,$,$.$,$,$.$,$,,,,..,,....,,,...,,.......,..,..,..,.,,,...c,..,,,......,...,,,.,,,,,,,C,.,.,,.,,,,,,....,,,..,.,,,,.,,,,,, C:IIII5II3IIIII95II/1.IIII>A5II4IA=)-)I>HIIDIIII-IIIII,III;IIII?:$III6=IIII8IIIIIII)IIIIII4I@IIIIII@=IIIIIIIIIDIIIIIID= 0 1 0 0 106 +chrM 987 988 A A 243 0 23 94 .$.$C$,$,$.......,..,..,..,.,,,...,,..,,,......,...,,,.,,,,,,,.,.,.,,.,c,,,,....,,,..,.,,,,.,,,,,,^!, I<%II,C21-@,IIGIIII==I+III%A2II<.IIIC/C$II$6EIIII9IIIIIIIIIIIIII3I6IIIII7@AIIIIIIIIIIIIGIIIIDI 0 1 0 0 80 +chrM 1005 1006 C C 138 0 18 49 .$,$,$,,,,....,,,..,.,,,,.,,,,,,,,,,,,,.,,,,,,a,,,,^!, 6IIIIII00@<III<IIIIIIIIIIIIIIIFI*I8IIIIII?IGII<&2 1 0 0 0 44 +chrM 1025 1026 G G 19 0 8 33 ,$t.,,,,,,,,,,,,,,,,,,,,,,,,,,,.., II.IIIIIIIIIIIIIIIIIIIIIB=@HIIIII 0 0 0 1 32 diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.10col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.pileup Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,1000 @@ +chrM 1 G G 25 0 25 1 ^:. I +chrM 2 T T 25 0 25 1 . I +chrM 3 T T 25 0 25 1 . I +chrM 4 A A 36 0 25 3 .^:.^:. II+ +chrM 5 A A 36 0 25 3 ... III +chrM 6 T T 36 0 25 3 ... III +chrM 7 G G 42 0 25 5 ...^:.^:. IIIII +chrM 8 T T 45 0 25 6 .....^:. IIIIII +chrM 9 A A 51 0 25 8 ......^:.^:. IIIIIIII +chrM 10 G G 54 0 25 9 ........^:. IIIIIIIII +chrM 11 C C 57 0 25 10 .........^:. IIIIIIIIII +chrM 12 T T 60 0 25 11 ..........^:. IIIIIIIIIII +chrM 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIIIIIIIIIIIIIIII +chrM 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chrM 15 A A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII +chrM 16 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 17 A A 87 0 25 20 .................... 9IIIIIIIIIIIIIIIIIII +chrM 18 A A 87 0 25 20 .................... @IIIIIIIIIIIIIIIIIII +chrM 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A +chrM 20 A A 54 0 25 20 ..................C. IIIIIIIIIIIIIII2II#$ +chrM 21 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 22 A A 87 0 25 20 .................... IIIIIIIIIIIIIIAIIIII +chrM 23 A A 87 0 25 20 .................... 9IIIIIIIIII0IIIIIIII +chrM 24 A A 87 0 25 20 ........N........... IIIIIIII"IIIIICIIIII +chrM 25 G G 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chrM 26 C C 57 0 25 21 .......A............. IIHIDII&IIIIIIIIIIIII +chrM 27 A A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII +chrM 28 A A 99 0 25 24 ........................ 1FIIIIIIIIIIIIIIIIDEIIII +chrM 29 G G 55 0 25 24 ..................NN.... ;IIIIII+HII=IIIIII""IIII +chrM 30 G G 68 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII +chrM 31 C C 105 0 25 26 .........................^!. =77&IFI&III>IIIIIIIIIIIIII +chrM 32 A A 105 0 25 26 .......................... /94$III:=IIH>@<G>ID5IIIIII +chrM 33 C C 105 0 25 26 .......................... CFE+IIIIII<IIIIIIII?IIIIII +chrM 34 T T 105 0 25 26 .......................... 9II+IIIIGII6I3IIIIE;IIIIII +chrM 35 G G 80 0 25 29 ...T......................^:.^:.^:. =G7'III9II4IIII9IIIIIIIIIIIII +chrM 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII +chrM 37 A A 82 0 25 30 ..C..........................^:. ?1'=GII?7E&5/0)IIIIIIIIIIIIIII +chrM 38 A A 94 0 25 30 ..C........................... 63+IIIA>I45IE9I>I:9IIIIIIIIIII +chrM 39 A A 117 0 25 30 .$.$............................ IFICE%*6I@39I=6IIIIIIIIIIIIIII +chrM 40 T T 111 0 25 28 ............................ $II292II5?<@2IEBDIIIIIIIIIII +chrM 41 G G 91 0 25 28 C........................... 3EII.>I:5IB4?IIIIIIIIIIIIIII +chrM 42 C C 80 0 25 29 T$.$..........................^:. #FF=-<I<IBIFAGAIIIIIIIIIIIIII +chrM 43 C C 108 0 25 27 .$.......................... I='9C/I@I>1IIIIIIIIIIIIIIII +chrM 44 T T 105 0 25 26 .$.$........................ 2GCII+>%<BHIEDIIIIIIIIIIII +chrM 45 A A 102 0 24 25 .$.......................^:. 0<,41'+'H<23IIIIDIIIIIIII +chrM 46 G G 99 0 24 24 .$....................... C@2FIA9HI>=IIIIIIIIIIIII +chrM 47 A A 96 0 24 23 .$...................... 1I0I&*B:+1IIIIIIIIIIIII +chrM 48 T T 93 0 24 22 .$.$.$.$.$.$................ +2&-6@:72III9IIIIIIIII +chrM 49 G G 78 0 24 17 .$...............^:. A=,IIIIIIIIIIIIII +chrM 50 A A 75 0 24 16 .$.$.............. >?I8II5IIIIIIIII +chrM 51 G G 72 0 24 15 ..............^:. IIIIIIIIIIIIIII +chrM 52 T T 72 0 24 15 ............... =IG(IIIIGEIIIII +chrM 53 A A 72 0 24 15 ............... I1D;IIIIIIIIIII +chrM 54 T T 40 0 24 15 .............N. IIIIIIIIIIIII"I +chrM 55 T T 72 0 24 15 ............... IIIIIIIIIIIIIII +chrM 56 C C 40 0 24 15 .............A. IIIIIIIIIIIII%I +chrM 57 T T 75 0 24 16 ...............^:. IIIIIIIIIIIIIIII +chrM 58 T T 75 0 24 16 ................ IIIIIIIIIIIIIIII +chrM 59 A A 50 0 24 16 ...............C IB20III:<DIII#II +chrM 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI +chrM 61 T T 72 0 24 15 ............... DIIIIIII=IIIIII +chrM 62 C C 53 0 24 15 .$.$.$..........A. ;IICIIIIIIIII3I +chrM 63 C C 63 0 24 12 ............ IIIIIIIIIII' +chrM 64 A A 35 0 24 12 ...........C 5III?1GIII-% +chrM 65 T T 63 0 24 12 .$........... IIIII>IIIIII +chrM 66 A A 60 0 24 11 .$.......... IHIC55III?I +chrM 67 A A 57 0 25 10 .......... 6=0@=IIIII +chrM 68 A A 57 0 25 10 .......... II:2III2>I +chrM 69 C C 57 0 25 10 .......... IIIIIII*2I +chrM 70 A A 33 0 25 10 .$.$.$....G.. II@,III#II +chrM 71 C C 48 0 25 7 .$...... IIII>06 +chrM 72 A A 45 0 25 6 .$..... IIIIID +chrM 73 T T 42 0 25 5 ..... II6-I +chrM 74 A A 42 0 25 5 ..... IIAI& +chrM 75 G G 42 0 25 5 ..... %IIII +chrM 76 G G 31 0 25 5 T..C. *II%I +chrM 77 C C 42 0 25 5 .$.... GIII, +chrM 78 T T 39 0 25 4 .... I#&3 +chrM 79 T T 39 0 25 4 .... IIF0 +chrM 80 G G 27 0 25 4 .$TT. I%&2 +chrM 81 G G 23 0 25 4 .C.^:. 61$I +chrM 82 T T 29 0 25 4 ..C. =4'I +chrM 83 C C 39 0 25 4 .... ,$*I +chrM 84 C C 28 0 25 4 .$A.. I$7I +chrM 85 T T 36 0 25 3 ... F+I +chrM 86 A A 2 0 25 3 .$CN &%" +chrM 87 G G 33 0 25 2 .. II +chrM 88 C C 19 0 25 2 .. 1$ +chrM 89 C C 33 0 25 2 .. @I +chrM 90 T T 28 0 25 2 .. #I +chrM 91 T G 3 9 25 2 GA )% +chrM 92 T T 33 0 25 2 .$. CI +chrM 93 T T 25 0 25 1 . I +chrM 94 T T 25 0 25 1 . I +chrM 95 A A 25 0 25 1 . I +chrM 96 T T 25 0 25 1 . I +chrM 97 T T 25 0 25 1 . I +chrM 98 A A 33 0 25 2 .^:. II +chrM 99 G G 33 0 25 2 .. II +chrM 100 T T 33 0 25 2 .. II +chrM 101 T T 33 0 25 2 .. II +chrM 102 A A 27 0 25 2 .. $9 +chrM 103 T T 36 0 25 3 ..^:. IIC +chrM 104 T T 36 0 25 3 ... III +chrM 105 A A 36 0 25 3 ... III +chrM 106 A A 36 0 25 3 ... III +chrM 107 T T 36 0 25 3 ... II5 +chrM 108 A A 39 0 25 4 ...^:. IIII +chrM 109 G G 39 0 25 4 .... II-I +chrM 110 A A 39 0 25 4 ..N. $I"I +chrM 111 A A 39 0 25 4 .... =I%I +chrM 112 T T 39 0 25 4 .... IIII +chrM 113 T T 39 0 25 4 .... IIII +chrM 114 A A 39 0 25 4 .... II0I +chrM 115 C C 28 0 25 4 ...G 3I=$ +chrM 116 A A 39 0 25 4 .$... IIII +chrM 117 C C 36 0 25 3 ... III +chrM 118 A A 36 0 25 3 ... I8I +chrM 119 T T 36 0 25 3 ... III +chrM 120 G G 36 0 25 3 ... '8I +chrM 121 C C 36 0 25 3 ... III +chrM 122 A A 29 0 25 4 ..C^:. <')I +chrM 123 A A 39 0 25 4 .... :%II +chrM 124 G G 28 0 25 4 .N.. I"II +chrM 125 T T 39 0 25 4 .... I1BI +chrM 126 A A 39 0 25 4 .... I?II +chrM 127 T T 28 0 25 4 ...N H/I" +chrM 128 C C 39 0 25 4 .... I=II +chrM 129 C C 28 0 25 4 .A.. D#II +chrM 130 G G 60 0 18 11 ....^:.^!.^:.^!.^!.^!.^!. 7(IIIIIIIII +chrM 131 C C 63 0 19 12 ...........^:. EC*IIIIIIIII +chrM 132 A A 72 0 17 15 ............^!.^!.^!. 7)IIIIGIIIIIIII +chrM 133 C C 78 0 17 17 .$..............^:.^!. I;IIIIIIIIIIIIIII +chrM 134 C C 81 0 16 18 ................^!.^!. IIIIIIIIIIIIIIIIII +chrM 135 C C 90 0 16 21 ..................^:.^!.^:. 7IIIIIIIIIIIIIIIIIIII +chrM 136 C C 105 0 18 26 .....................^:.^:.^:.^:.^:. 6IIIIIIIIIIIIIIIIIIIIIIIII +chrM 137 A A 103 0 18 26 ......................NNN. +IIIIIIIIIIIIIIIIIIIII"""I +chrM 138 G G 111 0 18 28 .$.........................^:.^!. &FIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 139 T T 114 0 19 29 ...........................^:.^:. DIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 140 G G 110 0 18 33 .............................^!.^:.^!.^!. 3IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 141 A A 108 0 18 33 ................................. ++IIIIIIIIIIIIIIIIIIIIIIIIIIIII#I +chrM 142 G G 105 0 18 35 .............T...................^:.^:. I/IIHIIIIIIII3IIIIIIIIIIIIIIIIIIIII +chrM 143 A A 86 0 18 41 .$.................................G^:.^!.^!.^:.^:.^!. IIEA,IIIIIIIIIIIIIIII=IDIIIIIIIIII#IIIIII +chrM 144 A A 105 0 18 42 ........................................^:.^:. IIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 145 T T 86 0 18 42 G......................................... %IIIIIIIIIII4IIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 146 G G 104 0 19 43 ..........................................^:. III:IIIIIIII.II&IIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 147 C C 104 0 19 45 ...........................................^:.^:. IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 148 C C 82 0 19 49 T............................................^!.^:.^!.^!. $IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 149 C C 82 0 19 49 .............................N................... .IIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIIIIIIIIIIIIIII +chrM 150 T T 99 0 19 51 .................................................^:.^:. IIIIIIIII=IIIIIII#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 151 C C 80 0 19 53 ..............................N....................^:.^!. IIIIIIIIIBIIIIIIIIIIIIIIIIIII&"IIIIIIIIIIIIIIIIIIIIII +chrM 152 T T 97 0 19 54 .....................................................^:. IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 153 A A 78 0 19 57 .............................T........................^!.^:.^:. D9I.=IIIIEIII=IAII9IIIIII@IIA$IIIIIBIIIIIIIIIIIIIIIIIIIII +chrM 154 A A 91 0 19 58 .......................................................NN^!. I4-'>I@FI85IIIDIIG?IIIIIIIII>IIIIIIIIIIIIIIIIIIIIIIIIII""I +chrM 155 A A 91 0 19 61 ..........................................................^!.^:.^:. <?;D=IIIICIIII9CBI=I0I)IAFIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIII +chrM 156 T T 96 0 19 62 .............................................................^:, IGI<IIIII8IIIII3IIIIIIIIIICIIIIIIIIIIII?IIIIIIIIIIIIIIIIIIIII& +chrM 157 C C 116 0 19 62 .$............................................................, IIIHIIIII>IIIIIIIIIIIIIII+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 158 A G 117 117 19 62 GGGGGGGGGGGGGGGGGGGNNNGGGGGG.GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGg^:g II6IIII<4I+IIIIIIII"""IIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII> +chrM 159 C C 127 0 19 62 ............................................................,, IIIIIIIIIIIIIIIIIIIIIIIAIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII/F +chrM 160 G G 136 0 19 63 ............................................................,,^:. II@AIII;7I2IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII +chrM 161 T T 135 0 19 63 ............................................................,,. BIB08IIIHEGI5IIIC5I49@I:6>IIICIIIIIIII14CIIII;IIIII@IIIIIIIII>I +chrM 162 C C 113 0 19 63 ............................................................,,. DIDIIIII(a)IFIIIIIIEIIIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII.-I +chrM 163 T T 134 0 19 63 ............................................................,,. <D:CIIII>III:IIII=IIIIIAIIII'IIIIIIIIIDIIIIIIIIIIIIIIIIII?III8I +chrM 164 C C 130 0 19 63 ............................................................,,. IIIEIIIIII@IIIIIFIIIIIIIIIII)IIIII>IIIIIEIIIIIIIIIIIIIIIIIII4FI +chrM 165 T T 116 0 19 63 .$.$.$.$.$.$.$............NNN......................................,,N IHC7IIII;FIIIIIED2I"""ICD=II:7IIIIIIIIGIIIIIIIIIIIIIIIIIIIIIII" +chrM 166 A A 122 0 20 56 C$....................................................,,. %41+I=:5I+'=//:9.,:;HI9+II6III4,I4II/5I;IIFI/IIIIIII:III +chrM 167 C C 122 0 20 55 .$.$.$.................................................,,A HI@IIIII@6IIIIIC@IIIIGIIIICIIIHDIIIIIIII@IIIIIIIIIII;6% +chrM 168 G G 146 0 20 52 .$.$...............................................,,. 7DIIII=IIIII5IIIII<IIAIAIFIIIIIIIIIIIIII=IIIIIIIDIII +chrM 169 A A 141 0 20 50 .$.$.............N...............................,,. 5.3%-8(1<6--(6,"%:G7I<6II163I@AI+CI?=IIIIIID9<IIII +chrM 170 T T 98 0 21 48 .$.$.$.NNN......................................,,A IE?I"""I<;:IIII=IIIBIIID>CHIHI>IIIIIIIIII>IIIII& +chrM 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 +chrM 172 A A 150 0 20 42 .....................................,,..^:. 3,.HHI?8I8IIIII<@.BI196@IIII4II&-HIHIIIIII +chrM 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII +chrM 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII +chrM 175 A A 141 0 20 38 .$.$.$.$.......................NN....,,... C0:2IAHIII*;5-HGI3G7I8:I1IF""IHIIIII#I +chrM 176 G G 82 0 21 34 .....NN......................,,... 3=824""DC5@;IH:%)III1II)&H7@3IIIII +chrM 177 G G 129 0 21 34 .$.$...........................,,... =823HAD6<:<IH,16I7,I4III8C,I8IIIII +chrM 178 A A 123 0 21 32 .$.$.$.$.$.$.....................,,... 97EII46:G.;I7I@III6IIC>:I>-IIIII +chrM 179 G G 105 0 21 26 .$.$...................,,... 9,DI3?I9I+-CCIAIIIIC3IIIII +chrM 180 C C 65 0 21 24 ...................,,..N III=3>&FHI>IIIIIIIIIIII" +chrM 181 A A 99 0 21 24 .$..................,,... II?I@I@>>I@IIIIIII/II(II +chrM 182 G G 55 0 20 24 .$.$..........NN....,,...^!. III64III7III""IIG=II>III +chrM 183 G G 93 0 20 22 .$.$.$.$............,,.... I;?79<IIIIIII:I-III@II +chrM 184 T T 81 0 21 18 ............,,.... &+I-I2EC9I72IIIIII +chrM 185 A A 81 0 21 18 .$.$..........,,..N. II@=IIF0DIDFIIII"I +chrM 186 T T 66 0 21 16 N$.$........,,..C. "4IIIIIIIIIIII&I +chrM 187 C C 32 0 21 14 .$.NN....,,.N.N HI""BI=8III"I" +chrM 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII +chrM 189 A A 33 0 21 10 .$...,,...C :I=BII$II( +chrM 190 G G 54 0 22 9 .$.$.$,,.... I9+III&II +chrM 191 C C 45 0 23 6 ,$,.... IIIIII +chrM 192 A A 42 0 22 5 ,.... IFII% +chrM 193 C C 45 0 23 6 ,$....^:. I&IIII +chrM 194 A A 45 0 20 6 .....^!. IIIIII +chrM 195 C C 45 0 20 6 .$..... IIIIII +chrM 196 T T 17 0 19 5 G.... <IIII +chrM 197 A A 42 0 19 5 ..... I<I&I +chrM 198 G G 42 0 19 5 ..... IIIII +chrM 199 A A 42 0 19 5 ....N IIII" +chrM 200 A A 42 0 19 5 N.... "IIII +chrM 201 A A 42 0 19 5 ..... <?III +chrM 202 G G 42 0 19 5 ..... 9I&II +chrM 203 T T 29 0 19 5 ..A.. $6$II +chrM 204 A A 42 0 19 5 ..... II+II +chrM 205 G G 42 0 19 5 ..... IIIII +chrM 206 C C 42 0 19 5 .$.... +GIII +chrM 207 T T 39 0 18 4 .$... IIII +chrM 208 C C 31 0 14 3 ... III +chrM 209 A A 10 0 14 3 .N. I"I +chrM 210 T T 31 0 14 3 ... III +chrM 211 A A 20 0 14 3 C.. 'II +chrM 212 A A 11 0 14 3 ... I&I +chrM 213 C C 20 0 14 3 ..A II$ +chrM 214 A A 31 0 14 3 ... II% +chrM 215 C C 31 0 14 3 ... DII +chrM 216 C C 31 0 14 3 ... ;II +chrM 217 T T 31 0 14 3 .$.. II$ +chrM 218 T T 28 0 18 2 .. II +chrM 219 G G 28 0 18 2 .. I; +chrM 220 C C 19 0 18 2 .A I% +chrM 221 T T 28 0 18 2 .. I' +chrM 222 C A 0 0 18 2 N. "A +chrM 223 A A 22 0 18 2 .. 4I +chrM 224 G G 28 0 18 2 .. II +chrM 225 C C 17 0 18 2 .. /I +chrM 226 C C 28 0 18 2 .. II +chrM 227 A A 10 0 18 2 .C 1: +chrM 228 C C 28 0 18 2 .$. II +chrM 229 A A 4 0 0 1 .$ I +chrM 264 T T 25 0 25 1 ^:. I +chrM 265 A A 4 0 25 1 N " +chrM 266 T T 31 0 14 3 .^!.^!. III +chrM 267 G G 39 0 18 4 ...^:. IIII +chrM 268 A A 39 0 18 4 .N.. I"II +chrM 269 A A 33 0 18 4 N... "III +chrM 270 C C 39 0 18 4 .... IIII +chrM 271 G G 17 0 18 4 NN.. ""II +chrM 272 A A 39 0 18 4 .... IIII +chrM 273 A A 33 0 18 4 ...N I+I" +chrM 274 A A 39 0 18 4 .... IIII +chrM 275 G G 39 0 18 4 .... IIII +chrM 276 T T 21 0 16 5 ...N^!. III"I +chrM 277 T T 42 0 16 5 ..... IIIII +chrM 278 C C 42 0 16 5 ..... 1IIII +chrM 279 G G 48 0 13 7 .....^!.^!. @IIIIII +chrM 280 A A 51 0 15 8 .......^:. HII;IIII +chrM 281 C C 54 0 17 9 ........^:. II'IIIIII +chrM 282 T T 32 0 17 9 .C....... I&I2?IIII +chrM 283 A A 54 0 17 9 ......... IIIAIIIII +chrM 284 A A 54 0 17 9 .....N... IIIII"III +chrM 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII +chrM 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II +chrM 287 C C 60 0 15 11 ........... IIG;IIIIIII +chrM 288 A A 52 0 15 11 ..NTC...... II"$1IIIIII +chrM 289 T T 34 0 15 11 ........N.. IIIII'II"II +chrM 290 A A 60 0 15 11 ........... H:IIIIIIIII +chrM 291 T T 34 0 15 11 ..N........ II"IIIIIIII +chrM 292 T T 60 0 15 11 ........... IIIIIIIIIII +chrM 293 A A 66 0 17 13 ...........^:.^:, I>IIIIIIIIIII +chrM 294 A A 66 0 17 13 ......N.NN.., I8%III"I""III +chrM 295 A A 59 0 18 14 ....C...G...,^:. BIII%III$IIIII +chrM 296 T T 69 0 18 14 ............,. 6II%IIII9%IIII +chrM 297 A A 69 0 18 14 ............,. H/IF'IIIIIIIII +chrM 298 A A 38 0 18 14 .........T..,. 0-IIIIIII3IIII +chrM 299 G G 72 0 18 15 .$...........,.^:, I%<IIIIIIIIIIII +chrM 300 G G 35 0 18 14 ....N....N.,., &IG2"IIII"II=I +chrM 301 G G 42 0 18 15 T$.$T..NC...N,.,^:. %E%II",III"IIEI +chrM 302 T T 69 0 19 14 .$........,.,.^!, $/IIIIIIIII3IB +chrM 303 T T 53 0 18 13 ..N..C..,N,., II"II#III"<I7 +chrM 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* +chrM 305 G G 66 0 18 13 ........,.,., DII8IIIIIIIII +chrM 306 T T 36 0 18 13 .......N,.,., .I#:IIB"IIBI6 +chrM 307 A A 41 0 18 13 ......NT,.,., II4III"&IIII/ +chrM 308 A A 66 0 18 13 ........,N,., I+III$I>I"III +chrM 309 A A 41 0 18 13 ......N.,C,., II6II+"II&III +chrM 310 T T 66 0 18 13 ........,.,., IIIIIIIIIIII= +chrM 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* +chrM 312 T T 63 0 19 12 .......,.,., IIIII+III?I9 +chrM 313 C C 69 0 19 14 .......,.,.,^!,^:. I-I4I?IIIII.AI +chrM 314 G G 38 0 19 14 .$.$..N..,.,.,,. I1I2"CIIIIIIII +chrM 315 T T 63 0 20 12 .$....,.,.,,. III9IIIIIIII +chrM 316 G G 60 0 20 11 .$...,.,.,,. DI=IIIIIIHI +chrM 317 C C 57 0 19 10 ...,.,.,,. IIIIIIIFII +chrM 318 C C 31 0 19 10 A..,.,.,,N %?IIIII.I" +chrM 319 A A 57 0 19 10 ...,.,.,,. '<IIIIIIII +chrM 320 G G 57 0 19 10 .$.$.,.,.,,. I.DIII?II# +chrM 321 C C 51 0 22 8 .,.,.,,. IIIII5II +chrM 322 C C 32 0 22 9 .,.,.a,.^:. IIIII%III +chrM 323 A A 40 0 22 9 .,.,.,,C. 6I=I4)F)I +chrM 324 C C 54 0 22 9 .,.,.,,.. IIIII%III +chrM 325 C C 54 0 22 9 .,.,.,,.. IIIIIIIII +chrM 326 G G 54 0 22 9 .,.,.,,.. FIII>BIII +chrM 327 C C 32 0 22 9 .,.,.,,.N IIII79II" +chrM 328 G G 54 0 22 9 .$,$.,.,,.. IIIIIIIII +chrM 329 G G 48 0 21 7 .,.,,.. IIBIIII +chrM 330 T T 48 0 21 7 .$,.,,.. HI9-III +chrM 331 C C 45 0 20 6 ,.,,.. I9IIII +chrM 332 A A 45 0 20 6 ,.,,.. I-IIII +chrM 333 T T 45 0 20 6 ,.,,.. I@IIHI +chrM 334 A A 30 0 20 6 ,$.,,C. I7II$I +chrM 335 C C 42 0 19 5 .,,.. 5II)I +chrM 336 G G 42 0 19 5 .$,,.. :II(I +chrM 337 A A 39 0 18 4 ,$,.. IIII +chrM 338 T T 36 0 20 3 ,.. III +chrM 339 T T 36 0 20 3 ,.. III +chrM 340 A A 36 0 20 3 ,.. IIA +chrM 341 A A 32 0 20 3 ,.. II% +chrM 342 C C 33 0 20 3 ,.. I&: +chrM 343 C C 36 0 20 3 ,.. I<I +chrM 344 C C 36 0 20 3 ,.. III +chrM 345 A A 32 0 20 3 ,.. II% +chrM 346 A A 36 0 20 3 ,.. IB6 +chrM 347 A A 32 0 20 3 ,.. II$ +chrM 348 T T 4 0 20 3 ,$.$A IIA +chrM 349 T T 9 0 25 1 . * +chrM 350 A A 20 0 25 1 . 5 +chrM 351 A A 25 0 25 1 . I +chrM 352 T T 25 0 25 1 . I +chrM 353 A A 33 0 25 2 .^:, II +chrM 354 A A 39 0 25 4 .,^:,^:, IFII +chrM 355 A C 14 36 25 4 .ccc IIII +chrM 356 T C 39 39 25 4 Cccc IIII +chrM 357 C C 39 0 25 4 .$,,, IDII +chrM 358 T T 36 0 25 3 ,,, 7:+ +chrM 359 C C 36 0 25 3 ,,, III +chrM 360 C C 39 0 25 4 ,,,^:, >II5 +chrM 361 G G 31 0 25 7 ,,,,^:,^:t^:, III=I$; +chrM 362 G G 35 0 25 7 ,,,,,t, IIIAI'/ +chrM 363 C C 48 0 25 7 ,,,,,,, IIIII%) +chrM 364 G G 57 0 25 10 ,,,,,,,^:.^:,^:, III5II>II9 +chrM 365 T T 57 0 25 10 ,,,,,,,.,, IIII>A9IEI +chrM 366 A A 57 0 25 10 ,,,,,,,.,, IIIIIIIIID +chrM 367 A A 60 0 25 11 ,,,,,,,.,,^:, IIIIIIIII<I +chrM 368 A A 63 0 25 12 ,,,,,,,.,,,^:, IIIIIIIIIIII +chrM 369 G G 63 0 25 12 ,,,,,,,.,,,, IIIIIIIII?ID +chrM 370 C C 35 0 25 12 ,,,,,,a.,,,, IIIII=%IIIII +chrM 371 G G 66 0 25 13 ,,,,,,,.,,,,^:, IIIDIIIII'IGF +chrM 372 T T 66 0 25 13 ,,,,,,,.,,,,, BIIIIII%III@C +chrM 373 G G 38 0 25 14 ,,,,,,,.,,n,,^:, IIIIIIIII."CII +chrM 374 T T 75 0 25 16 ,,,,,,,.,,,,,,^:,^:, IIIIIIIIIIIA8GIE +chrM 375 C C 51 0 25 19 ,,,,,a,.,,,,,,,,^:,^:,^:, III1I%4II2I/4II01*& +chrM 376 A A 90 0 25 21 ,,,,,,,.,,,,,,,,,,,^:,^:, IIIIIIIIIIIIIIIIIDIII +chrM 377 A A 93 0 25 22 ,,,,,,,.,,,,,,,,,,,,,^:, IIIIIIIIIIIIBIIIIIIIII +chrM 378 A A 93 0 25 22 ,,,,,,,.,,,,,,,,,,,,,, IIIIIIICIIIIIIIIIFIIII +chrM 379 G G 93 0 25 22 ,,,,,,,.,,,,,,,,,,,,,, IIIIII?IIIIEIIIIIIIIGI +chrM 380 A A 99 0 25 24 ,,,,,,,.,,,,,,,,,,,,,,^:,^:, IIIIIIIIIDII;IIIIIIIIIII +chrM 381 C T 77 108 25 28 tttttttTttttgttttttttttt^:t^:t^:t^:t IIIIIIIIIIII&I7CI>BCA296+IA1 +chrM 382 T T 117 0 25 30 ,,,,,,,.,,,,,,,,,,,,,,,,,,,,^:,^:. IIIIIIIIIIII,IIII>II5GI>;H=BCI +chrM 383 A A 82 0 25 30 ,,,,,,,.,,g,,,,,,,,,,,,,,,,,,. IIIIIIIIII%%4IIIIIII#IIIIIIIII +chrM 384 A A 76 0 25 30 ,,,,,,,.,c,,g,,,,,,,g,,,,,,g,. IIIIIIIIIIII$IIIIIII$IIIIF,4II +chrM 385 T T 123 0 25 32 ,,,,,,,.,,,,,,,,,,,,,,,,,,,,,.^:,^:, IIIIIII$IIII<III$(-I0FIIIIII>I00 +chrM 386 A G 88 120 25 32 gggggggGggnggggggggggggggggggGgg III>IIIIII"I&IIIIIIIIIIII?IIDI94 +chrM 387 C C 69 0 25 32 ,,,,,,,.,,,,,,,,,,,,,,a,,,nn,.,, IIIIIIIIIII?&III7-IIII+BII""II3. +chrM 388 C C 123 0 25 32 ,$,,,,,,.,,,,,,,,,,,,,,,,,,,,,.,, IIIDIIIIIII@)IIIIIIIII+)I/II0I<= +chrM 389 A A 85 0 25 31 ,$,$,,,,.,,,,,,,,,,,t,,,,,,,,,.,, IIIIIIIIIIIBIIIIII&>IIIIHIIIIII +chrM 390 A A 114 0 25 29 ,,,,.,,,,,,,,,,,,,,,,,,,,,.,, IIIIIIIII$IIIIIIIIIIIIIIIIIII +chrM 391 A A 74 0 25 29 ,,,,.,,,,,,,,,gg,,,,,,,,,,.,, IIIIIIIII9III$+$IIIIIIIIIIIII +chrM 392 A A 114 0 25 29 ,,,,.,,,,,,,,,,,,,,,,,,,,,.,, IIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 393 T T 114 0 25 29 ,,,,.,,,,,,,,,,,,,,,,,,,,,.,, IIIIIIIIIII@GII%IIIIFCII>/III +chrM 394 A A 117 0 25 30 ,,,,.,,,,,,,,,,,,,,,,,,,,,.,,^:, IIIIIIIII;IIIIIIIIIIIIIIII>III +chrM 395 A A 117 0 25 30 ,$,,,.,,,,,,,,,,,,,,,,,,,,,.,,, IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 396 A A 114 0 25 29 ,$,$,$.,,,,,,,,,,,,,,,,,,,,,.,,, IIIIIIII*IIIIIIIIIIIIIIIIIIII +chrM 397 G G 71 0 25 26 .,,,,,,,,,,,,,,,,,,c,,.,,, IIIIIIIIIIIIIIIIIII#*IIII, +chrM 398 T T 84 0 25 26 .,,,,,,,,,,,,,,,g,,,,,.,,, III/I1IIIIIIII;I+III)IHII4 +chrM 399 T T 105 0 25 26 .$,$,$,,,,,,,,,,,,,,,,,,,.,,, IIIIIIIIIIIIIIIIII3IIIIII' +chrM 400 A A 96 0 25 23 ,,,,,,nnn,,,,,,,nn,.,,, II7III"""IIIIIII""I>III +chrM 401 A A 63 0 25 23 ,,,,,,g,,,,,,,,,,,,.,,, IIIIII&%#IIIIIIIIIIIIII +chrM 402 A A 96 0 25 23 ,$,,,,,,,,,,,,,,,,,,.,,, IIIIIIIIIIIIIFIIIII8III +chrM 403 A A 96 0 25 23 ,$,,,,,,,,,,,,,,,,,.,,,^:, I,IBIIIIIII45C;IIIIII1G +chrM 404 C C 60 0 25 22 ,,,,,,,,,,,,,,,,,.,,t, IIIIIIIIIIIIIIIIIIII$= +chrM 405 C C 93 0 25 22 ,,,,,,,,,,,,,,,,,.,,,, IIIIIII4IIIIIIIIIIII:8 +chrM 406 C C 63 0 25 23 ,$,,,,,,,,,,,,,,,,.,,a,^:. AIIIIIIIII4IIIIIIIII&8I +chrM 407 A A 93 0 25 22 ,,,,,,,,,,,,,,,,.,,,,. IIIIIIIIIIIIIIII@IIIII +chrM 408 G G 93 0 25 22 ,$,,,,,,,,,,,,,,,.,,,,. IIIIIIIIIIIIIIIIDII5:I +chrM 409 T T 90 0 25 21 ,$,$,,,,,,,,,,,,,.,,,,. IIIIIIIII+IIIII)II<=I +chrM 410 T T 84 0 25 19 ,$,$,$,,,,,,,,,,.,,,,. IIIIIIIIIIIIIIII&6I +chrM 411 A A 81 0 25 18 ,$,$,,,,,,,,.,,,,.^:.^:. IIIIIIIIIIFIII;III +chrM 412 A A 75 0 25 16 ,$,,,,,,,.,,,,... IIIII//I:II?DIII +chrM 413 G G 72 0 25 15 ,,,,,,,.,,,,... IIIIIII?III4III +chrM 414 C C 75 0 25 16 ,,,,,,,.,,,,...^:. IIIIIIIFII?&IIII +chrM 415 C T 75 75 25 16 t$t$tttttTttttTTTT IIIIIII>II93IIII +chrM 416 G G 72 0 24 15 ,$,$,$,$,.,,,,....^!, IIIII9II-4IIII@ +chrM 417 T T 60 0 24 11 ,$.$,,,,...., I/II8CIIIID +chrM 418 A A 54 0 24 9 ,,,,...., IIII/IIII +chrM 419 A A 54 0 24 9 ,,,,...., IIII/IIII +chrM 420 A A 54 0 24 9 ,$,$,,...., IIII2IIII +chrM 421 A A 48 0 23 7 ,,...., I4FIIII +chrM 422 A A 48 0 23 7 ,,...., II2IIII +chrM 423 G G 57 0 24 10 ,,....,^:.^:.^:. 1IIIIIIIII +chrM 424 C C 34 0 23 11 ,,....,...^!a IIIIII8III% +chrM 425 T T 66 0 23 13 ,,....,...,^:.^:. II$IIIIIII2II +chrM 426 A A 66 0 23 13 ,,....,...,.. II/IIIIIII=II +chrM 427 C C 49 0 23 15 ,,....,..T,..^:.^:. IIIIIIIII''IIII +chrM 428 A A 46 0 23 17 ,,G...,...,....^:.^:. II"IIIIII%IIIIIII +chrM 429 A A 81 0 24 18 ,$,....,...,......^:. IICI.IIIII7IIIIIII +chrM 430 C C 78 0 23 17 ,....,...,....... IIIIIIIII0IIIIIII +chrM 431 C C 49 0 23 18 t....,...,.......^!, $IIIIIIII1IIIIIII) +chrM 432 A A 84 0 23 19 ,....,...,.......,^:. IFII0IIIIIIIIIIIIII +chrM 433 A A 56 0 23 19 ,C...,...,.......,. I'IIIIIIIIIIIIIIIII +chrM 434 A A 60 0 23 22 ,....,...,.....T.,.^:.^:.^:. IC4=DIIIIIIIIII&IIIIII +chrM 435 G G 96 0 23 23 ,....,...,.......,....^:. IIGCIIIIIIIIIIIIIIIIIII +chrM 436 T T 65 0 23 24 ,A...,...,.......,.....^:. I$5@7II;IGII$IIII1IIIIII +chrM 437 A A 105 0 24 26 ,....,..N,.......,......^:.^:. I#.&IIIH"IIIIII@IIIIIIIIII +chrM 438 A A 69 0 24 29 ,$CCC.,...,.......,........^:.^:.^:. I#)*IIIIIIIIIIIIIIIIIIIIIIIII +chrM 439 A A 88 0 24 30 TGG.,...,.......,...........^:.^:. '%$IIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 440 A A 120 0 24 31 ....,...,.......,.............^:, $8-?IIEIIIIIII<IIIIIIIIIIIIIIII +chrM 441 T T 85 0 24 31 A$...,...,.......,............., $IBIIIIIIIIIIIII/IIIIIIIIIIIIID +chrM 442 A A 126 0 24 33 ...,...,.......,.............,^:,^:.^:. II1IIBIIIIIIIIIIII/IIIIIIIIIII2II +chrM 443 G G 91 0 24 33 ...,...,.......,.............,n.. IIIIIII@IIIII9IIIIIIIIIIIIIIII"II +chrM 444 A A 126 0 24 33 ...,...,.......,.............,,.. I@1IIIIAIIIIIIIIIIIIIIIIIIIIII+II +chrM 445 C C 100 0 24 36 ...,...,.......,.............,a..^:.^:.^:. IH>IIIIIIIIIIIIIIIIIIIIIIIIIIG#IIIII +chrM 446 T T 103 0 24 37 .$.$.,...,.......,.............,g.....^:. IIHIIII.II7IIIIIIIIIIIIIIIIII(&IIIIII +chrM 447 A A 141 0 24 38 .,...,.......,.............,,......^:.^:,^:. 2II/II>I5IIIIIIIIIIIIIIIIIII(IIIIIII%I +chrM 448 C C 144 0 24 39 .,...,.......,.............,,.......,.^:. 8IIIIIBIAIIIIIIIIIIIIIIIIIII%IIIIIII'II +chrM 449 G G 126 0 24 45 .$,...,.......,..T..........,,.......,..^:.^:.^:.^:.^:,^:. 1IIIIIIIIIIIIIII)IIIIIIIIIII2II>IIII,IIIIII:I +chrM 450 A A 162 0 24 45 ,...,.......,.............,,.......,......,.^:. II7II3:I7I8IIIIIIIHIIIIIIII=II*IIIIIIIIIIIIII +chrM 451 A A 168 0 24 47 ,$...,.......,.............,,.......,......,..^:.^:. I>EII?I1IH3IIII$DIIIIIIIIII+IIIIIII1IIIIIIIIIII +chrM 452 A A 175 0 24 49 ...,.......,......N......,,.......,......,....^:.^:.^:. IE@I8I8IIIIIIIIIII"IIIIIII5IIIII5/IIIIIIIIIIIIIII +chrM 453 G G 178 0 25 53 ...,.......,.............,,.......,......,.......^:.^:.^:.^:. I>IIIIIII*IIIIII9IIIIIIII:8IIIII@I&IIIIIIIIIIIIII-III +chrM 454 T T 134 0 25 54 ...,.......,.............g,.......,......,...........^:. ,**I0I./I'(I2IIC1IE/>IFII'%II6D<$I3IIIIIIFIAIIIII(IIII +chrM 455 G G 168 0 25 54 ...,.......,.............,,.......,......,............ IEIIHIIII>IIIIII4IIIIIIIII+IIIIIII$IIII.IIIIIIIIIIIIII +chrM 456 A A 173 0 25 54 ...,.......,.............,,.......,......,............ :1+IDB<II@IIIIICIIIGIIIIII+IIIIIII/IIII$>IIIIIIIIIIIII +chrM 457 C C 154 0 25 56 ...,.......,.............,g.......,......,............^:.^:. I63I<IAGI8IIIII=IIIIIIIIII$IIIIIII3IIIH$IIIIIIIIIIIIIIII +chrM 458 T T 205 0 25 59 .$.$.$,.......,.............,,.......,......,..............^:,^:,^:, IAII@IIIIIIIIIIIBIIIIIIIII,IIIIIII:IIIIIIIIIIIIIIIIIIIIIB*H +chrM 459 T T 160 0 25 56 ,$.......,......N......,,..N....,......,..............,g, IAI4II-%IIIIIII"IIIIIII2II"IIII4IIIIIIIIIIIIIIIIIIIII3$I +chrM 460 T T 205 0 25 59 .$.$.....,.............,,.......,......,..............,,,^:.^:.^:.^:. IIIBIBIIIIIIIIIIIIIIII.IIIIIIICIIIIIIIIIIIIIIIIII+III8?IIII +chrM 461 A A 202 0 25 62 .....,......N......,,.......,......,..............,,,....^:.^:.^:.^:.^:. I:I58IIIIGID"III.III&IIDIIDIIIIIIIIIIIIIIIIIIIIIIII)IIIIIIIIII +chrM 462 A A 182 0 25 64 .$.$...,.............,,.......,......,..............,c,.........^:.^:, B<I,GIIIIFIC=IIIII?I-IIB@?IIIIIIIIIIIIIIIIIIIIIIIII%IIIIIIIIIIII +chrM 463 T T 164 0 25 63 .$.$.,.............,,.......g......,..............,g,..........,^:, I+:IIIIIII;?IIIIII8IIIIIII)IIIIIIIIIIIIIIIIIIIII;%9IIIIIIIIIII6 +chrM 464 A A 218 0 25 65 .$,.............,,.......,......,..............,,,..........,,^:.^:.^:.^:, >IIIIBII,IIIIIII%IIIIIII&IIIIIIIIIIIIIIIIIIIII.I1IIIIIIIIIIIIIIII +chrM 465 C C 169 0 25 65 ,.............,,.....A.,......,..............,,,..........,a...,^:A IIIIBI>H1IIIIB$)IIIII$IIIIIIIIII0IIIII6IIIIIIHIIIIIIIIIIIII&IIICI +chrM 466 C C 175 0 25 67 ,$....A........,,......N,......,..............,,,..........,,...,.^:.^:. IIIF@%BIIIIIIFI+IIIII'"@IIIIIIII$IIIIIII@IIIII;IIIIIIIIIIII0IIIIIII +chrM 467 T T 194 0 25 67 .$............,,.......,......,..............c,,..........,,...,...^:. IAIBIIBHIIII7I3IIA=H$IIIIIIII6IIIIIIIIIIIIII,I,IIII&IIIII5'III9IIII +chrM 468 C C 205 0 25 66 ............g,.......,......,..............,,,..........,,...,.N.. II>IIIIIIIIA&'IIIHIIIIIII&&'IIIIIIIIIIIIIIIIIIIIII&IIIII?(IIIII"II +chrM 469 T T 207 0 25 66 .$.$.$.........,,.......,......,..............,n,..........,,...,G... III>I44EIIICI@IIEDC$IBIIII(IIIIDIIII@IIIIII1"0IIII%IIIIII1III7IIII +chrM 470 G G 198 0 25 65 .$........n,.T.....,......,..............,,,..........,,...,....^:.^:. /+.2IIIIH"II4HFI7IIIIII(III?II<II@II=IIIIIIII$IIIIIIIIIIII1IIIIII +chrM 471 A A 194 0 25 68 N$.......,,.......,...C..,.......C......,,,..........,,...,.N....^!.^:.^:t^:, "I95IDC0IIB?00/#6I:II%0(III-IIII#IIDIII:FIIIIIIIIIIIIIIIIII"IIIIII$? +chrM 472 C C 187 0 25 72 .$.$.....,t.......,....A.,..............,a,..........,a...,A.......,,^:.^:.^:.^:.^:. I@IIIIII&IIIFG6IIIIII$IIIIIIIII$IIFIIII:IIIIIIIIIIII%IIII,IIIIII/I-IIIII +chrM 473 T T 237 0 25 74 .$.$.$..,,.......,......,..............,,,..........,,...,........,,.....^:,^:.^:.^:. IIII?I&IIF:9&$;@IIIIIII)IIIIIIIIIIII?IEIIIIIIIIIIIIIIIIIIIIIIII57IIIII+III +chrM 474 A A 208 0 25 73 .$.$,,.......,....C.,..............,,,..........,,...,........,,.....,...^:.^!, @9II@;G79*0IIDII&IIII6IIII3IIIIII?IIIDIIIIIIIIIIIIIIIIIIIIII+IIIIIIIIIIII +chrM 475 C C 238 0 25 74 ,$,.......,......,..............,,,..........,,...,........,,.....,....,^:.^:.^:. III<@IIFIIIIII9III+IIIII)IIIIIII&IIIIIIIIIIII/IIIIIIIIIIII87IIIII7IIII:III +chrM 476 A A 225 0 25 76 c.......,....T.,..............,,,..........,,...,........,,.....,....,...^:.^:.^:. 2ID???#>I8II$#'III9II=?(AB2III@III3IIIIIGIIIIIII?IEIIIIIH8IIIIIIIIIII=IIIIII +chrM 477 C C 240 0 25 77 ,$.$.$.....,......,..............,,,..........,,...,........,,.....,....,......^:. IIIIAC6DIIIII%IIIIIIIII&IIIIII6IIIIIIIIII)IIIIIIIIIIIIIIIIIIIIIIFIIII9IIIIIII +chrM 478 G G 204 0 25 77 .....,....T.,.......T......,,,..........,,...,........,,.....,....,.......^:.^:.^:. 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IIICIIII,II?>0III&I"IIIIII5III)9AIIIIIIIIIIIIIIIIAIIIIIII +chrM 530 C C 161 0 22 57 ,$...,,,..,,....,,.,.....,,..,,n,,,,,,..,,,...,,,,,.,,,,,. I0IIIIIIIIIIII9II3IIIIIIIIIIII"III<IIII=9FIIIBIB0/FI))%)I +chrM 531 T T 196 0 22 56 .$.$.,,,..,,....,,.,.....,,..,,,,,,,,,..,,,...,,,,,.,,,,,. 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IIIIIIFIIIIII9IIIIIIIIII4IIII +chrM 551 A A 82 0 22 30 ..,,,..G,,,,,.,,,,,.,,,,,,.,.^!, BIIIII="IIIII9IIIIIIIIIIGIIIII +chrM 552 A A 82 0 22 30 .$.$,,,..C,,,,,.,,,,,.,,,,,,.,., CIIII;D+IIIII<IIIIIIIIIIIIGII= +chrM 553 G G 77 0 22 28 ,$,$,$.$.A,,,,,.,,,,,.,,,,,,.,., III&I#IIIII)IIIIIIIIIIIII;I< +chrM 554 C C 99 0 22 24 ..,,,,,.,,,,,.,,,,,,.,., I$IIIII9IIIIIIIIII=IIBII +chrM 555 T T 85 0 22 25 .$G,,,,,.,,,,,C,,,,,,.,.,^:. B#IIIII0IIIII&III@IIIII1I +chrM 556 A A 74 0 22 27 T$,$,,,,.,,,,,.,,,,,,.,.,.^:.^:.^:. "IIIIIIIIIIICIIIIIIIIIIIIII +chrM 557 T T 108 0 23 27 ,$,,,.,,,,,.,,,,,,.,.,....^:.^:. IIIIDIIII,.III@IIIII1IIIIII +chrM 558 T T 83 0 23 27 ,$,$,$.,,,,,.,,,,,,.,.,....G.^:. III+IIIIIII>IHDIG4I4IIIIIII +chrM 559 C C 71 0 22 26 N$,$,$,$,,.,,,,,,.,.,.......^:.^:. "IIIIIIIIIIIIIIIDIIIIIIIII +chrM 560 G G 93 0 23 22 ,,.,,,,,,.,.,......... IIIIIIIIIIIIIIIIIIIIII +chrM 561 C C 96 0 23 23 ,$,$.,,,,,,.,.,.........^:. IIIIIIIIII8IIIIIIIIIIII +chrM 562 C C 93 0 23 22 .,,,,,,.,.,..........^:. IIIIIIIIIIIIIIIIIIIIII +chrM 563 A A 93 0 23 22 .,,,,,,.,.,........... *IIIIIIIIIIIII=IIIIIII +chrM 564 G G 93 0 23 22 .$,,,,,,.,.,........... IIIIIII9IIIIIIIIIIIIII +chrM 565 A A 90 0 23 21 ,,,,,,.,.,........... IIIIII4IIIIIIIIIIIIII +chrM 566 G G 60 0 23 22 ,,,,,,C,.,...........^:. IIIIII#IIIIIIIIIIIIIII +chrM 567 T T 60 0 23 22 ,$,,,,,A,.,............ IIIIII+IIIIIIIIIIIIIII +chrM 568 A A 57 0 23 21 ,,,,,T,.,............ IIIII$IIIIIIIIIIIIIII +chrM 569 C C 96 0 23 23 ,,,,,.,.,............^:.^:. IIIIIEIIIIIIIIIIIIIIIII +chrM 570 T T 68 0 23 23 ,$,$,$,$,.,.,........C..... IIIII=IIIIIIIIIII(IIIII +chrM 571 A A 84 0 23 19 ,$.,.,.............. IIIIIIIIIIIIIIIIIII +chrM 572 C C 81 0 23 18 .,.,.............. ;IIIIIIIIIIIIIIIII +chrM 573 T T 84 0 23 19 .,.,..............^:. C?IIIIII2IIIIIIIIII +chrM 574 A A 87 0 23 20 .,.,...............^:. 7IIIIIDEIII=IIIIIIII +chrM 575 G G 87 0 23 20 .$,.,................ 0I7IEIIIIIIIIIIIIIII +chrM 576 C C 84 0 24 19 ,.,................ AII>III5IIIIIIIIIII +chrM 577 A A 93 0 24 22 ,.,....N...........^:.^:.^:. III.III"IIIIIIIIIIIIII +chrM 578 A A 99 0 24 24 ,.,....N..............^:.^:. I:III??"III&IIIIIIIIIIII +chrM 579 C C 102 0 24 25 ,.,.....................^:. III=I??IIIIIIBIIIIIIIIIII +chrM 580 A A 105 0 24 26 ,$.,...................NN.^:. III>IEHII;8I@7IIIIIIII""II +chrM 581 G G 105 0 25 26 .$,.......................^:. 0I>I?3FIIIIIIIIIIIII<IIIII +chrM 582 C C 111 0 25 28 ,........................^:.^:.^:. IBI@@IIIEIIIIIIIIIIIIIIIIIII +chrM 583 C C 68 0 25 29 ,...................NN......^:. IIIBBIIIIIIIIIIIIIII""IIIIIII +chrM 584 T T 114 0 25 29 ,............................ IIIII3IIIIIIIIAIIIIIIIIIIIIII +chrM 585 A A 114 0 25 29 ,............................ IIC5<,DF7I=IIIIIIIIIIIIIIIIII +chrM 586 A A 114 0 25 29 ,$....N....................... II:81"HCHIB=IIIIIIIIIIIIIIIII +chrM 587 A A 114 0 25 29 ....N.....................N.^!, 7G;<"7DBI;:GIIIIIIIIII6III"IA +chrM 588 A A 80 0 25 29 ......................C....., 6I//III2IH@FIIIIIIIIII%IICII0 +chrM 589 C C 117 0 25 30 ............................,^:. CI66II6IIIFIIIIIIIIIIIIIII&I6I +chrM 590 T T 117 0 25 30 .$...........................,. 8I98II23IHIBIDIIII<IIIAIIIII&I +chrM 591 C C 120 0 25 31 .$.$.$........................,.^:.^:. IIIII>BII?IIFIIIIGI/IIIIII$IIII +chrM 592 A A 85 0 25 31 .$.$....................C.,...^:.^:.^:. II37IA0IIF@IIIIIII6III#I<IIIIII +chrM 593 A A 117 0 25 30 .$.....................,......^:. @I3E4II=6IIICIAIIIIIIIIIIIIIII +chrM 594 A A 82 0 25 30 .$N$...........C.......,.......^:. ,"<<FIACIII?,(I=IIII'IIIIIIIII +chrM 595 G G 114 0 25 29 ...................,........^:. AII67IIIIICBIIIIIIIIIIIIIIIII +chrM 596 G G 87 0 25 30 .$..T..............Nt.........^:. @7I%5III7IIIIIIIII")IIIIIIIIII +chrM 597 A A 120 0 25 31 .$.................,..........^:.^:. :>4E<IIIG<5I=IIIII&IIIIIIIIIIII +chrM 598 C C 123 0 25 32 .................,............^:.^:. IIIIIIIIIIIIIIIII.IIIIIIIIIIIIII +chrM 599 T T 129 0 25 34 .................,..............^:.^:. ;46CIICIC;IIIIIII>IIIIIIIIIIIIIIII +chrM 600 T T 130 0 25 35 .................,................^:. ?18III>9>9IIIIIII&IIIIIIIIIIIIIIIII +chrM 601 G G 103 0 25 37 .$................,...............C.^:.^:. I3GIIC8.EHIIIIIII&IIIIIIIIIIIIIII&III +chrM 602 G G 126 0 25 38 ................,...................^:.^:. *?III?;=<I>III,49I(IIGBIIIIIIIIIIIIIII +chrM 603 C C 106 0 25 40 ..............A.,.....................^:.^:. I;IIII6III?III$IIIIIIIIIIIIIIIIIIIIIIIII +chrM 604 G G 112 0 25 41 T$.$...........N..,.......................^:. -IGII59I7I=II"(I$I8IIIIIIIIIIIIIIIIIIIIII +chrM 605 G G 106 0 25 40 .............N,........................^:. IIIIFIIIIIIII"II&IIIIIIIIIIIIIIIIIIIIIII +chrM 606 T T 97 0 25 41 .G............,............G............^:. ($50#(+4/D-++#<0II.*9II4III&I1IIIIIIIIIII +chrM 607 G G 105 0 24 43 ..............,....T..T..................^:.^!, BI-&*1&6IIIGIIII%;9I.;>IIIIIIIIIIIIIIIIIII3 +chrM 608 C C 118 0 24 45 .$.............,...........................,^:.^:. $;#&10..-+8IG9I6E&7"DHI=IIIIIIIIII3IIIIIII6II +chrM 609 T T 103 0 24 48 .$...........N,...........................,..^:.^:.^:N^:. D<7;<7HI93<I"IIIA8II@IIIIIIIIIIIIIIIIIIIICIIII"I +chrM 610 T T 120 0 24 49 ............,...........................,......^:.^:. I>.IIIIIIIIIII&IIIIIIIIIIIIIIIIIIIIIIIII;IIIIIIII +chrM 611 T T 120 0 24 50 ............,...........................,........^:. ID=IIIIIII#IIIIIIIIIIIIIIIIIIIIIIIIIIIII=IIIIIIIII +chrM 612 A A 99 0 25 51 .$.$.$...T.....,...........................,.........^:. 6+&-.6%,I;7DI5I$FCI9I8III:EI-IIIIIIIIIIIIIIIIIIIIII +chrM 613 C C 101 0 24 49 .$.$.......,..T....N...................,..........^:. *+4))48$@(6%%+)0-"%BII4IFBIIEIIIIIIIIIIIIIIIIIIII +chrM 614 A A 112 0 24 50 .$......,...........................,...........^:.^:.^:. &*0+-I0I(00)0+*I.,1I(II=I.*III&IIIIIIIIIIIIIIIIIII +chrM 615 T T 99 0 24 49 .$....A,.........A.................,...........N.. )B8IG%I,E2,/;;I.#II9?I;II=IIIIIIII2IIIIIIIIIII"II +chrM 616 C C 104 0 24 49 .$....,...........N...............,..............^!, B23.E%84%1-C55E@I"10ICIIEIIIIIIIIIIIIIIIIIIIIIIII +chrM 617 C C 104 0 24 48 .$.$.$.a...........................,.............., IIBI$3IB<%IIII<IIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 618 C C 106 0 24 48 N$,...........................,..............,^:.^:.^:. "I@&-7*HIIIIIIIIIIIIIIIIIIIII@IIIIIIIIIIIIIIBIII +chrM 619 T T 117 0 24 48 ,.........C..C..............,...........N..,...^:. I2&-+)(4I+>CI$&I15@IIIIIIIII,IIIIIIIIIII"II5IIII +chrM 620 C C 106 0 24 48 ,...........................,..A...........,.... I>I$F428I0@II;IDDIIIIIIIIIIIGII&IIIIIIIIIIIIIIII +chrM 621 T T 102 0 24 50 ,...........................,...........N..,....^:.^:. I7$D)/&2C/0<I)I*+@7IIIIIIIII/IIIIIHIIIII"II-IIIIII +chrM 622 A A 102 0 24 52 ,$.CT.........TC.............,..............,......^!.^!. I(#$%$'$&.I8+%$/2+>:=;=<IIIHIDI0IIIII5IIIIIIIIIIIIII +chrM 623 G G 90 0 23 55 ..T.T.............T........,..............,........^!.^:.^!.^!. '(%,%*$2.(=&%%69??%IIIIIIAIDII%I<FII8IIIIIIIIIIIIIIIIII +chrM 624 A A 91 0 23 56 .$..........................,.....C........,............^:. )%#2-:-9$+D/)16.0I&DDB=III7A4IIII#<I?IIIIIIIDIIIIIIIIIII +chrM 625 G G 93 0 23 57 ...T......................,..............,.............^!.^:. +$3&86I,4@I7%=@II+III7IIIIIIIII+IIIBIIIIIII%IIIIIIIIIIIII +chrM 626 G G 103 0 23 58 .$.$..........T.............,..T...........,...............^!. '0%)A.9II>=82>IIH%IDIIIIGIIII$IIIIIIII4IIIIIIIIIIIIIIIIIII +chrM 627 A A 91 0 23 57 .$.$.$............C........,..............,................^:. $*+30&+,.(;4)+0+@IGH1II=I6I:GI5@I5IIIHIII2IIIIIIIIIIIIIII +chrM 628 G G 108 0 22 57 .$...........A........,..............,................A^!.^!.^:. 5GI<=4;>G=I<%IIIIII.IIII'IIIIIIII$IIIIIIIIIIIIIIIIIIIIIII +chrM 629 C C 89 0 22 61 .$.....T....T........,..............,....................^!.^!.^:.^:.^:. 13;AI&$</?4+IIGEIIIIIIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 630 C C 100 0 22 60 .$..................,..............,.........A............... E7II)&BCII:IIIIIIIIIIIIII+IIIIIIII$IIIIIIIII-IIIIIIIIIIIIIII +chrM 631 T T 90 0 22 63 .$.................,.....C........,.........................^:.^:.^!.^!, ,G:(1&&I*1IDAAIIIIIIIIII%IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 632 G G 112 0 22 66 .$.$......T........,..............,............................,^:.^:.^:.^:, ,A')+66>%III?IIIIIII*II1IIIIIAIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 633 T T 133 0 22 65 .$C$.............,..............,............................,...,^:, 2$->G2I4G<>HIIII@IIIIII:>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 634 T T 164 0 22 66 .$.$...........,.....N........,............................,...,,^:.^:,^:, 3BIEIIIIIIIIIIIIIII"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIIIIII< +chrM 635 C C 174 0 22 65 .$..........,..............,............................,...,,.,,^!. 43-HIA==IIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2I +chrM 636 C C 157 0 22 67 .$.$........,..............,............................,...,,.,,.^!.^:.^:. G?IGIIEIIIIIIIII2IIII<IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII+II9*IIII +chrM 637 A A 187 0 21 68 .$.$......,..............,............................,...,,.,,....^:.^!.^:, 3F./:II1I>;IC=%G<<>II=III.I?IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII:IIIIIII +chrM 638 T T 186 0 21 67 .$.$....,..............,............................,...,,.,,......,^!. IFIIIIIIFIII/IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII5IIIIIIII +chrM 639 A A 187 0 21 70 .$...,..............,............................,...,,.,,......,.^!.^:.^!.^:.^:. I8III>I40III66=IIIIIIIHBIIIIIIIIIIIIIIIIIIII?IIIIIIIIIIIIIIIIIIIIIIIII +chrM 640 A A 185 0 21 70 .$..,..............,............................,...,,.,,......,......^!. >III9<.BI0;;.?IIIIII&I=DIIIIIIIIIIIIBIEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 641 T T 184 0 21 69 .$.,..............,............................,...,,.,,......,....... III<IIII4GIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IIIIIIIIIII;5IIIIII?IIIIIII +chrM 642 C C 185 0 20 71 .$,$..............,............................,...,,.,,......,.......^!.^!.^!. IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;IIIIIIIIIIIIIIIII +chrM 643 G G 161 0 20 71 .$.$............,.T..........................,...,,.,,......,..........^!.^:. :6%@I7IIII/III,I'I6IIIIIII1IIIIII0IIII7>IIIIII=IIII0IIIIIIIIIIIIIIIIIII +chrM 644 A A 151 0 20 71 .$.$.$.$........,............................,...,,.,,......g............^!.^:. 9/G$2I&878=III&I:II88IIIIBIIII=IIIIII;IIIIIIIIIII>IIIIII$IIIIIIIIIIIIII +chrM 645 T T 155 0 20 69 .$.$......,............................,...,,.,,......,.............A^:.^:. II5IIIIIIIAI8IIIIIIIIIIIIIGIIIIIIIIIIIIIIIII%DIIIIIIIII%IIIIIIIIII$II +chrM 646 A A 162 0 19 72 .$.....,............................,...,,.,,.....T,................^:.^!.^!.^!.^!. 96III3II+IAIIIGIIIIIIIIHIAIIFGEFIIIIIIIIIIIAIIIII#IIIII'+IIIIIIII>IIIIII +chrM 647 A A 166 0 19 71 .$....,............................,...,,.,,.....Nn.........N........... <IIAIII%I.IIHIIIIIAIIIIIIIIIFI5%(IIIIIIIIIIIIIII""IIIIIIIII"IIIIIIIIIII +chrM 648 A A 163 0 19 70 .$...,.......................C....,...,,.,,......,.T.C................. I4?6II.B.II@@IIII5IIIH7GDIIB.C84IIII'III8?IIIIIIII%I&I8IIIIIIIIIIIIIII +chrM 649 C C 164 0 19 69 .$.$.$,............................,...,,.,,......,.N.N.....N........... IIIII#IIIIIIIIIIIIIIIH@IIIIIIIIIIIIIIIIIIIIIIIIII"I"IIIII"IIIIIIIIIII +chrM 650 C C 162 0 18 66 ,............................,...,,.,,......g..................... II/I:IIIIIIIIIIIIIIIIIII&IIIIIIIIIIIIIIIIIII.IIIIIIIIIIIIIIIIIIIII +chrM 651 C C 164 0 18 68 ,$...........A................,...,,.,,......,.....................^!.^:, II/I9IIIIIII%FIIIIIIIIIFI@IIIIIII;III?IIIIIIIIIIIIIIIIIIIII9IIIIIII% +chrM 652 C C 179 0 19 67 ............................,...,,.,,......,......................, IIIBIIIII2IIIIIIIIIIIHA4E&'IIIII8II:FIIIIII*IIIIIIIII)IIIIIIIIIIIII +chrM 653 G G 156 0 19 67 .$.$.$......................NN.,...,,.,,......,......................, IDH9IIIIIII0FIIIII7III>E=""IIIII+II*III@IIIIIIII.@IIIIIIIIIIIIIIIII +chrM 654 A A 171 0 18 65 .$...................C....,...,,.,,......,......................,^:, 38I5:II@I.II=I50I64<&+3&>I5III&IHIGIIFIIIEIIIIIIIBIIIIIIIIII5AIII +chrM 655 T T 167 0 18 64 ........................,...,,.,g......,......................,, IIHBIIII478III5IIH6&8&%4IIII9IA5&IIIII8IIIIIIIIIIIIIIIIIIIIIIIIC +chrM 656 A A 172 0 18 65 .$.$...................C..,...,,.,n......,......................,,^:. IIIIIIII:IIII5=IIB=;,&$1IIIIIIII"6IBII%IIIIIIIIIIIIIIIIIIII;IIIII +chrM 657 A A 171 0 18 64 .$.$....................,...,,.,,......g......................,,.^:. E5IICI.>I?IIH/I:104IGIIFIIIIHII7III:+&IEIEIIIIIIIIIIIIIII=FIIIII +chrM 658 A A 137 0 19 62 .$.$.$.$.............CC.,...,,.,,......,.C.C..................,,.. 83<I1>8<0;1II+200%%)I/CIIII&F3<II?III$B&IIIIFIIIIIIGIII=GIIIII +chrM 659 C C 197 0 19 59 .$...............,...,,.,,......,......................,,..^:. IIIII*>IID>+=IIIIIIIIII+ICIIIIII<IIIIIIIIIIIIIIIIIIIIIIIIII +chrM 660 C C 166 0 19 58 .$.$.............,...n,.,,......,......................a,... /CII>9@II277IIII9II"IIIIIIFIIIIIIBIIIIIIIIIIIIIIII$II7IIII +chrM 661 C C 126 0 19 57 .$.........NN.t...,n.,n......,......................,,...^:A II=4IIII;I""I%@III"II"II@IIIIFIIIIIIIIIIIIIIIIII7IIIII%I# +chrM 662 C C 161 0 19 57 .$...........,...n,.,,......,.....T................,,.A..^:. I9AIIIFHFIII2III"IIIIDIHII#III1I3$IIIIIIIIIIIIIIIIIII&I#I +chrM 663 A A 161 0 19 57 .$.$.$...C....,...,n.,,......,.........N............,,.....^:. 1+3>+$$%**/I-CII":I+&75I1@III51III89"I.FIE?EC5/,IIIIIIIII +chrM 664 C C 170 0 20 54 .$.$.$.$.$...,...,,.,,......,..T...................a,...... IIIICIIII>IIIIII<FIII?II@)##IIIIIIIIIIIII6I8II(IIII<II +chrM 665 C C 175 0 20 49 ...,...,,.,,......,......................,,...... )-CIIIIIIIII8F>IIIIEI9IIIIIIIIIIIIIIIIDIIIIIIIIII +chrM 666 A A 175 0 20 49 .$.$.$,$...n,.,,......,......................,,...... ,-.I+II"IFII9/.?,II0I6IBIG5=6=>4IIHG;5.-IIIIII6II +chrM 667 T T 112 0 20 45 .$.$N$,$n.,,......,......................,,...... II"I"&2I9@0I/1I0IIGI/I>A+<(D<I)/F6&0IIIIIIIII +chrM 668 C C 153 0 19 42 ,$.,,......,......................,,......^!, IIIIHBGI@IIHIIIIIIIIIII=IIIIII$IIIIIIIIIII +chrM 669 C C 135 0 19 42 .$,$,$......,.....................Ga,......,^:. IIIIIII@IIFI@IIIIIIIII;IIIIHIII56IIIIIIIAI +chrM 670 C C 144 0 18 39 .$.....,......................,,......,. II:IHIIIIC6IIIEIIIIIII<IIIAIIIIIIIIIIII +chrM 671 T T 108 0 19 39 .$.$.$..,.........A............,,......,.^:. <<I55II/D0).516$HIHII2?$2+,IIIIIIIIIIII +chrM 672 T T 100 0 19 36 .$.$,$......................,,......g.. C,I8+<-II<553?DI6I/-A3(/IIIDIIIII$II +chrM 673 G G 94 0 18 34 .$....................T,,......,..^!, )IIIIII9AIIG?II.<I511+IIIII+IIDII+ +chrM 674 C C 126 0 18 33 .$.$.$.$.$................,,......,.., IAIIIIIIIII=>II%IG$EIIIIIIIIIIIII +chrM 675 T T 80 0 19 29 .$..............N,,......,..,^:. (AFIII2II,3I2)2"I$IIIIII*IIFI +chrM 676 A A 117 0 19 30 ...............,,......,..,.^:.^:. 7+>0?71I0,.+*%IIIEHI)?2IIIIIII +chrM 677 A A 98 0 19 30 .$.$.$............,,...T..,..,... ;0/07*.I22')(+IIIIII.IICIIHIII +chrM 678 T T 108 0 20 27 .$.$..........,,......,..,... I7A@I/&+<7;IIIIIIIII&IIIIII +chrM 679 T T 68 0 21 25 .$.$.....C..,,......,..,... ;:I*'-7$5I<IEII&II%II3III +chrM 680 C C 105 0 21 26 .$.$......,,......,..,...^:.^:.^:. I<7IE7CIIIIIIFIIIIIIIIIIII +chrM 681 A A 105 0 21 26 .$.$.$.$.$.,,......,..,......^!,^:. /&.'*#IIAII0IIIIIIIIIIIIII +chrM 682 G G 51 0 23 23 A,n......,..,......,.^:.^:. %0"IIIIIIIEIIIIIII>CIII +chrM 683 C C 63 0 23 23 .,,...N..,..,......,... $IIIII"IIIIIIIIIIII6III +chrM 684 C C 74 0 23 27 .,n......,..,......,...^:.^:.^:.^:. <I"III%IIIIIIIIIIIIIIIIIIII +chrM 685 T T 108 0 23 27 .,,......,..,......,....... $II?II)I:IIIEI??II$=IIIIII6 +chrM 686 A A 71 0 23 30 C$,$,......,..,.....C,.......^!.^:.^:. /II49I)9I)IIIIIIII#IIIIIIIIIII +chrM 687 T T 114 0 23 29 ,......,..,......,..........^!. IAIIIII3IIIIIIIII&IIIIIIIIIII +chrM 688 A A 114 0 23 29 n......,..,......,........... "4II=21II>IIIIIIIIIIIIIIIIIII +chrM 689 T T 129 0 22 34 ,$......,..,......,...........^!.^:.^!.^:.^!. IIIIIIIIII:I65II1IIIIIIIIIIIIIIIII +chrM 690 A A 106 0 22 36 ......,..,......,......T....N....^:.^:.^:. @IIIIIIB9CIIHIII2IIIIII*II&I"IIIIIII +chrM 691 C C 103 0 22 37 .$.....,..,......,.........A.........^:. IIIIIIIIIIIIIIIIIIIII,IIII(IIIIIIIIII +chrM 692 C C 147 0 23 43 .$....,..,......,....................^:.^:.^:.^:.^:,^:.^:. II?IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 693 G G 140 0 22 42 ....,..,......,........................,.. I/87I/IIIIIII5IIIIIIIIIIIIIIIIIIIIIIIII3II +chrM 694 C C 128 0 23 44 .$...,..,......,........................,..^:.^:. IIIIIIIIIIIII8IIIIIIIIIIIIIIIIIII<IIIII'IIII +chrM 695 C C 128 0 23 48 ...,..,......,........................,....^:.^:.^!.^:.^:. 7IIIIIIIIIIIIIIIII>IIIIIIIIIIIIIIIIIII*IIIIIIIII +chrM 696 A A 141 0 23 50 .$..,..,......,........................,.........^:.^:. *9II06II89IIIIIIIIIIIIIIICI&I&IIIIIIIIBIIIIIIIIIII +chrM 697 T T 105 0 22 50 .$.,..,.....C,........................n...........^!. @6IFFIIF<7I'CII6IIIIIIIIIIIIIIIIIIIII"IIIIIIIIIIII +chrM 698 C C 101 0 22 50 .$,..,......,........................n............^:. IIIIIIIIII(IIIII9IIIIIIIIIIIIIIIIIII"IIIIIIIIIIIII +chrM 699 T T 140 0 22 52 ,..,......,........................,.............^:.^:.^:. IIIIIIIEIG=IIIIIIIIIIIIIIIIIIIIIIIIAIIIIIIIIIIIIIIII +chrM 700 T T 121 0 23 55 ,..,......,.........N..............,................^:.^:.^:. IIIII@4FIIIIIIIIIIII"IIIIIIIIIIIIII?$IIIIIIIIIIIIIIIIII +chrM 701 C C 146 0 23 59 ,..,......,........................,...................^:.^:.^:.^:, IGIIII>II$IIIII)IIIIIIIIIIIIIIIIIII0IIIIIIIIIIIIIIIIIIIIIII +chrM 702 A A 136 0 23 62 ,..,......,........................,.......C..............,^:.^:.^:. I00I4954I#I6I1I+IIIIIIIIIIIII=IIIII?IIIIIII%IIIIIIIIIIIIIIIIII +chrM 703 G G 137 0 23 64 ,$T.,......,........................,......................,...^:.^:. I%7"III=I/IIIDIIIIIIIIII8I*IIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIII +chrM 704 C C 115 0 23 68 .$.,......,........................a......................,.....^:.^:.^:.^:.^:. H>)IIIGI#IIIIIIIIIIIIIIIIIIIIIIIII1IIIIIIIIIIIIIIIIIIIIII*IIIIIIIIII +chrM 705 A A 135 0 23 68 .,......,..C.....................,......................,..........^:. :I@9:4I&I9I&IIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 706 A A 117 0 23 71 .$,.....C,........................n......................,...........^:.^:.^:. IIIIF,:)IA9IIAIIIIIIIIII<H7IIIIII"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 707 A A 115 0 24 78 ,......,........................nC.....................,..............^:.^:.^:.^:.^:.^:.^:.^:. II15DI.I4IHIIII@I<II=IIIIIIIIIII"&IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 708 C C 141 0 24 79 ,$......,........................,......................,......................^:. II;?IIIIIIII$IIIIAIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIII'II2IIIIIIIII$IIIIIIIIIIIII +chrM 709 C C 120 0 24 79 ......,............N...........,......................,.........T.............^!. IIIIIDIII*@6IIIIIII"IIIIIIIIIIII*II?IIIII$IIIIIIIIIIII+IIIIIIIII#IIIIIIIIIIIIII +chrM 710 C C 112 0 24 81 .$.....,............N...........,......................t........................^:.^:. I,48I>IIIII1IIIIIII"IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII$IIIIIIIIIIIIIIIIIIIIIIIIII +chrM 711 T T 106 0 24 84 .$.$...,...........N............,......................,..........................^:.^:.^:.^:. >*+F8IBI/IIIIIIAI"+IIIIIIIIIII5I3IIIIIIIIIIIIIICIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 712 A A 116 0 24 83 ...,....CC..................,......................,..............................^:. 4I+I:I&I$.IEI:I,I&I)>GI8IC,DIIIIII8IIA<II4IIIIIIIII+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 713 A A 141 0 23 92 ...,........................,......................,...............................^:.^!.^:.^!.^:.^!.^:.^:.^:. .F3I0FIIICIBI-EDII3I=71III>IIIFCII7IGHIIIIIIIIIIIII8IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHII +chrM 714 A A 127 0 23 96 ...,..C.....................,......................,............................C...........^:.^:.^:.^:. 67'II>(IIIAFI<IIIII?I$EI>GAGII4III8IIDIIIDIIIFIIIIG$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 715 C C 113 0 23 98 .$.$.$,....A...................,......................g............................................^:.^:. 7I=IIIDI)IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII@IIIIIIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 716 A A 128 0 23 97 ,$.$.C.....................,......................,..............................................^:.^:. IHI-I'?6:II=IIIIIB:IE?B3FIIIIII:AIA+I=IIDI0IIII&IIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 717 A A 124 0 24 98 .$.$.........C...........,......................,................................................^:.^:.^:. III51I@II?I+I250A2EIIIIIII9II95I5>IIII3IIIIIIIIIIIIIIFIIIIIIIIIIIIIAIIIIIIIIIIIIII%I$IIIIIIIIIIIII +chrM 718 G G 127 0 24 98 ........NN..T........,......................,.........N.........................................^:.^:. III9III7""II&IIIIIHIGIIIIIIIIIIIII7IIIIIIIII9IIIIIIIII"IIIIIIIIIIIIIIIIIIIIIIIII.I&IIIIIIIIIIIIIII +chrM 719 G G 117 0 24 98 .$.$.$.$.....N...........,......................,..................................................... ='=IIII=I":40=II&ID+CIIIIIIBIIIIIIIIIIIIIIII1IIIIII7IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 720 T T 130 0 24 96 .....C...........,...C.....G............,............G....................A...................^:.^:. D?76/$I'@'<,I7;I<I5GI'H+B.3%;=<3II1CGIIB@FII8@II0II4II$IIIII537IIIIIIIIIII#IIIIIIIII=III$IIIIIII +chrM 721 A A 124 0 24 97 .$.$.$............T.,......................,.......................................................^:. II?>II'>&E?BAI<%<III?IIIIG42IIIIIIEIIIIIIIIIBIII+IIIIIIIIIIIAI/IIIIIIIIIIIIIIIIIIIIIIIII$IIIIIIII +chrM 722 C C 126 0 24 94 .$.............,......................,.....................................................T.. III(I%FIFIIIIIIIIIII:IIIFI9IEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIIIIIII+II +chrM 723 C C 128 0 24 97 N............,......................,........................................................^:.^:.^:.^:. "IIIICI=III8GIIIIIIIIIHIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 724 G G 129 0 24 99 .$C$.$.$.$........,......................,.................................................C......N...^:.^:. I#@E6IIIIII=II-IIIII@HI*IIIIBIIIIDIIIIIIIIIHIIIIIIIIIIIIIIIIIIIII1IIIIIIIIIIIIIIIIIIII$IIIIII"IIIII +chrM 725 A A 139 0 24 95 .$.$.$.....,......................,..............................................................^:. *7AII.(.I+2F4<1=5/*IDI,;I4;D7GIIIII5II?9IIIIGIIIIII::6II1BIIIIIII+IIIIIII0IIICIIII3I%IIIIIIIAII +chrM 726 A A 126 0 24 92 C$....,......................,....................................C.......................... $=I<II7I3B61-2)I=1H4-I9IIICCI@AI:II9ICIIIIIHIIIF995II<IIIIIIIIIII(IIIIIIIIIIIIIIIIIIIIIIIIII +chrM 727 G G 122 0 24 94 .$.$.$.$,$.$.$....................,.........................................N.....................^:.^:.^:. ;2/2IIIIIIII:III8IFIIIIIII?3IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII<IIIIIII"IIIIIIIIIIIIIIIIIIIIIIII +chrM 728 T T 122 0 24 87 ....................,.................................................................. F1F@@<4-I23>I8+@AII8I@'93HI4IDG<IIIIIIIG98>FI@@II=IIIIIIIIIIBIIIII<:IIIIIIIIIIIIIIIIIII +chrM 729 A A 123 0 24 96 .$.$..................,..................................................................^:.^:.^:.^:.^:.^:.^:.^:.^:. IID5239HI@4I*I6IIIIII:II;III7IIIIIIIIII0494III=IIIIBIIIIIII@I3IIIII;IIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 730 A A 100 0 24 99 .$.$.$.$.$.............,.................................C.............N..................N........^:.^:.^:.^:.^:. C)49,II6I4<II44;@I%III/B089:<II1=IIII@56/III<IIII>II3II'IEIIIIII?H"II@IIIII/IIIIIIIII"IIIIIIIIIIIII +chrM 731 G G 81 0 24 94 .$.$...........c................................................................................ &I<2III8II+IA#FIICII2IIHII*I>I2I?ECHIIIGII&IIII79IDIIIIIIIIIIII*IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 732 C C 109 0 24 95 .$..........,................................N.N.N...........................................^:.^:.^:. .IIID7II>IIIIII?IIDIAIAIIIIIIIIBDBIIIIIIHIII"I"I"IIIIIIIIIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 733 A A 108 0 24 96 .$.........,....................................C..............................................^:.^:. 9/:II665III=HI:II=I;IFII7III>35;EIIIFFI6IIIIIII%IIIE&IAIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII,IIIII +chrM 734 C C 113 0 24 95 .$.$.$......,..................................................................................... GIIIII%II.IDI<IIIIIIFIIIIIIIIAF>III?IIIIIIIIIIIICIIIIIIIHIIIBII&IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 735 A A 123 0 24 95 .$.$.$...,.....................................................................................^:.^:.^:. IHH6I4IIII4II7&II2IIIIIII9/4,9IIIIIAICIII:IIIIB>HIBII=III'IIIIGIIIIIIIIIIIIII8IIIIIIIIIIIIIIIII +chrM 736 A A 106 0 24 97 .$.$.$,$.........................................N........................C.....................^:.^:.^:.^:.^:. 19%I/II<GICI501I<6>IIII3-3=II9@=@IC>I5GIII>EA"III?DIIIIIIIGIIIIIIIIIII$IIIIIIIIIIII.IIIIIIIIIIIII +chrM 737 A A 98 0 24 98 .$.$.$..............................C................T.......................C..................^:.^:.^:.^:.^:. AI709I4I>IDII.7IIC+938AEC5?IDIC5I*IIII7I21?5B1AIII#IIIIIIIIIIAIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 738 T T 87 0 24 99 .$.$................................................C...............................N............^:.^:.^:.^:. 0IDI.II3IIAIIIII978=II?II0IDIIIIIIII:IIIII;CIII.II%IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIIIIIIIIIIII +chrM 739 A A 98 0 24 97 .$.$.$.$.$............................................................................................ I9ID;HIIICIIEI0002II6BG<I8II+IIII7B:1IICI=III$IIICIIIIII$IIIIIIIIIIIIIIIII&IIIIIIIIIIIIIIIIIIIIII +chrM 740 T T 87 0 24 93 .$..............................N.......C...C................................................^:. 4I7IIIIII2.3I+I8I=-IIIIIAI<III8"III69II%5II'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 741 C C 101 0 24 92 .$.$.$......................................................................................... IIIIIIIIIIIIII=II,IIIIIIIIIIIIIIIIIIIIIAI;IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 742 C C 85 0 24 92 .$.$.$.$.$.$.$.$............................N.....................A..............................^:.^:.^:. IIII+87AIIIAIIGIHIIIIIIIIII?IIIIIIII"IIIIIIIIIIIIIIIIIIIII(I<IIIIII9IIIIIIIIIIIIIIIIIIIIIIII +chrM 743 A A 88 0 24 86 .$..............C........................T...................................N.......^:.^:. =IC7<C@I4III7IH,IE>IA-:+6IIIIIII=IIIIII=%IIIIIIAIIIIIIIII%IIIIIIIIIIIIIIIIII"IIIIIIIII +chrM 744 A A 101 0 24 85 .$.................................................................................... IIIICIIIIIIIIIII?HIIIII=III(IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 745 C C 84 0 25 86 .$.$..............................N.........................................N.........^:A^:. B5IE/I<IIIIICIGIA>ICII8C8I9IIIII"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIIIII0I +chrM 746 A A 83 0 25 86 .$.$.$.$................................C...............................................^:.^:. 3+:FA>4A?I=I5I1(AI524I:<IEIDI0IIIII=$IIIIIIIIIII9AIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 747 T T 83 0 25 83 .$..................................................C..............................^:. 3IF('I:4-?+IH1I2-@G7IIII3IIIIIIGAIIIIIIIIIIIIIIIIII%IAIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 748 A A 97 0 25 86 .$.$C$.$.$.$.$.$.$.........................................................................^:.^:.^:.^:. ?DIIIII<I8I@>B2IIFB%IIIIIIHIII;4III3IIIEEIIIIIIIIIIIIIIIIIIIIIIIIII$IIIIIIIIIIII@IIIII +chrM 749 A A 85 0 25 80 .$N$.$.$......C...........N...................................................N..^:.^:.^:. 6"IIA0DI4)'III?>IBIIE<"IIIIIIIII3IIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>II"IIIII +chrM 750 A A 93 0 25 77 .$.$............................C......C......................................^:. I2GII,II%@IAIIIII9IIIIIIIIIDII>I>II=IIIIIIIIIIIIIIIIIIIIIIIII8IIIII.IIIIIIIII +chrM 751 A A 87 0 25 78 .$.$..................N...G..................................................^:.^:.^:. IIII5:HII>IIIII<IGII"III&IIIIIIIIIII>IIIIIIIIIIII/GII9EIIIIIIIIIIIIIIIIIIIIIII +chrM 752 A A 101 0 25 77 .$.$.$.....N...................................................................^:. 1+5=>I1D"II3I6IIIIIIAII;II0IIIIIII6@IIIIIIIIIII+IIIIIIIIIIIIIIII5IIIIIIIIIIII +chrM 753 C C 87 0 25 76 .$.$.............................................................N..........^:.^:. II>9II9IHHEIIBIIIGEII&I+=IIIIIIIIIIIIIIIIIIIIIIIIIIIII8IIIIIIII"IIIIIIIIIIII +chrM 754 G G 102 0 25 82 ..........................................................................^:.^:.^:.^:.^:.^:.^:.^:. I95IIIIII>IIIIIIIII?IIIIIIBIII.7IIIIIIIIIIIIII$IIIIIIIIII3@IIIIIIIIIIIIIIIIIIIIIII +chrM 755 T T 92 0 25 84 A$.$.......G....................C.....................G........N..C.................^:.^:. %:32+II8+#86I6)&I@44II6IIIIIIB)IIIII='HII59IIII>IIII%IIIIIIII"II.IIIIIIIIIIIII%IIIII +chrM 756 T T 86 0 25 82 .$.........................C....................................................... 4IAII+C%IFII67IIFIIII<IIII(>5IIIIIFIIIIIIIIIIIIIII&IIIIIIIIIIIIIIIII7IIIIIIIIIIIII +chrM 757 A A 85 0 25 84 N.....C....................................N.......C.............................^:.^:.^:. "3III.%?<IIII5I>IIBHAII-II5:I1IIEIIIIIIIIII"IIIIIII(III0IIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 758 G G 84 0 25 84 .$.$.$.$......N......................................................................... IIIIIG0DIH"IIID29I1IIII0IIG/*I.IIIIFIIIIIII0IIIIIIIIIII4IIIIIIIIIIIII:IIIIDIIIIIII3& +chrM 759 G G 92 0 25 82 .$.$N...........T.......................N.........................................^:.^:. 4B"IFIIIIIIE6G'I7IIIIII09IHIII4IIIIIII"DIIIIIIII>II;IIIIIIIII/IIIIIIIIIIIIIIIIIIII +chrM 760 T T 106 0 25 86 A$.....A..............G........................A........G........................^:.^:.^:.^:.^:.^:. #6<EF9$330.II4*;EII7+$I;II:3IICB4073I6;IEIIII5+II@IIIII:I+IIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 761 C C 85 0 25 85 .........A.......NN.................................................................. FIIII=II4+II;8IIA""3@FIIIIIIIIIIEIIIIIIIIIII?III.IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII&III +chrM 762 A A 100 0 25 86 .$.$.$..................................................................................^:. IHIIH*7:H,IH50AIIII*1EBII@/@:IFI@IIII=IFIIIHBIII6II'CI5I9I-A/IIIIIIIIIIIIIIIIIIIIIIIII +chrM 763 A A 99 0 25 83 N........................................................................C......... "IC:6,1III=CIIIIB6GIII7G<DI>IIIIII8IIII$IHIII=I&IIIIIIIIIIIIIIIIIIIIIIII39IIIIIIIII +chrM 764 G G 107 0 25 86 .$.$.$.$.$.$.$.$T$.....NN......................................AN...........................^:.^:.^:. 9I9I@8I4-I7IC&""=&=I+II=>I>IIIIIIIIIIIII@IIII+IIIIIIIII"II%IIIII@IIIIIIIIIIIIIIIIIIIII +chrM 765 G G 88 0 25 77 .$.$.$.$.$.T..T.T............................................N.................... :,I;&I7D.%I'III<HD7IIIII*CIIIIIIIIII%IIIIIIIIIIIIIIIHIII"IIIIIIIIIIIIIIIIIIII +chrM 766 T T 88 0 25 72 ................................N..........C............................ I%.&IIII93+;8;/&<@II(IIII2E3I@I3"9ICIII(II:/7I9IIIIIIAI;EIIIIIIIIIIIIIII +chrM 767 G G 86 0 25 74 .$.$.$...T.....................................T...........................^:.^:. II>+3A%IAEC7:FI@II/IIIIIIIIIII%.IIIIIIIFIIII)IIIIIIIIIIIGIIIIIIIIIIIIIIIII +chrM 768 T T 102 0 25 71 .$.$................................A.................................... &IBGII@5ICF>0?BII2IIIIII@+II;IEIII7I,III8IIIIIIIIIIIE@IIIIIIII8IIIIIIII +chrM 769 A A 104 0 25 73 .....................................................................^:.^:.^:.^:. IGI;DIHIBII<EII7IIII%<BIII-IIIEIIIIIII:IIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 770 G G 87 0 25 75 .$.$.$...................................................T..................^:.^:. I9I:5CIC9IIIIII:IIAI0I<;II-IIIIIII?IB2-III?IIIIIIIIIII)IIIIIIIIIIIIIIIIIIII +chrM 771 C C 102 0 25 75 .$.$.$.$.$...................................................................^:.^:.^:. IIIII@;2FDCIIIIIII>40II&IIIII*IDII3,?IIIIIEIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 772 C C 88 0 25 71 .$.$.$.$.$...........................N.....................................^:. IA<I;II<IIII>II4II&IIIIIIIEIIA)I"IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 773 C C 91 0 25 67 .$.$.$.$..........A........N.................T........................^:. I?IEIII$IC:II#%IIII>III"II.IIIIIIIIIIH=II$IIIIIIIIIIIIIIIIIIIIIIIII +chrM 774 A A 103 0 25 64 ...............................................................^:. :II%H6/3I2%II8C8>5=&?8,II5IH:IIIICDII1II=HI4IIIIIII5IIIIIIIIIIII +chrM 775 T T 106 0 25 66 .$...............................................................^:.^:. III:C=III/=FIC2II<IIB<III2IIIIIII?=II6IIIIIIIIIIIIIEIIIIIIIIIIIIII +chrM 776 G G 106 0 25 65 ................................................................. III97HII+IIIIIIIDIII0?II@IIIIIIIEBIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 777 G G 94 0 25 65 .$.$.$...............N..T........................................... HI<I=II@,IIIIII9=I"II,IIFIIHIIFII8IIII1IIIIIIIIIIIIIIIIIIIIIIIIII +chrM 778 G G 108 0 25 63 .$.$...T.....C......T...................T.......................^:. AG(II$IIIII&6BIII:'IIIII9IIIII=IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 779 A A 99 0 25 66 .................C...........................................^:.^:.^:.^:.^:. +II&/*B,8,33I1.&80GII-6III214?9IID=III?IIII(I?IIIIIIIIIIIIIIIIIIII +chrM 780 T T 105 0 25 68 .$.$................................................................^:.^:. II93IHIII%I;HI?1>@?AIGIIIII6I=IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 781 G G 89 0 25 66 .$.$.N.........................................................A.... I+G"IIII(a)IIIII.IIIIIBIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII%IIII +chrM 782 G G 100 0 25 65 .$........T..T................C..................................^:. IIIIII<II-II0II3II4IIIIIAIIII%II3IIIIIIIIIIIIIIIIIIIIIIIIIBIIIIII +chrM 783 A A 92 0 25 68 .$.$.$.$....T.....C.....T......................C....................^:.^:.^:.^:. @9.8&7.=#.+I32$I).II&1*6.75;97III0III@CE:II&;III@IIIIIIIIIIIIIIIIIII +chrM 784 G G 88 0 25 65 .$.$.$........................N....................................^:. 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";4%IIIII=II?IA2II+I'IIIIIIIII$IIIIICIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 787 A A 88 0 25 65 .$............G................................................^:.^:.^:. :E?48/DII/11.$IID/5III1IIII6BIIIGI7GIIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 788 A A 128 0 25 66 .$.$..............N...............................................^:.^:, IC3=-*IHI(a)=7.I+I";III?IIIIIIAII@;III<IIIIIIIIIIIIIIIIIIIIIIIIIIII= +chrM 789 A A 112 0 25 67 .$.$.$.$.$.$.$.$......C.........N......................................c^:.^:.^:, ?;16II=C3/0?EI&=8II8GIII"I?=IECIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII$III +chrM 790 T T 120 0 25 60 .$.$....C..C.............................................g..,^:. 127III&II%IBIIIIIIDIII@I?IIIIIIIIIIIIIIIIIIIIIIIIIIIIII&IIAI +chrM 791 G G 155 0 25 60 .......T.............................................,..,.^:T^:, 7III5II$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II/ +chrM 792 G G 168 0 25 64 .$.$.$.C..C.............................................,..,..,^:.^:,^:,^:, EIII&IC'IAIIII4IG?IIIIIIIIIIIIIII8IIIIIIIIIIIIII6IIIIIIIIII-I8II +chrM 793 G G 195 0 25 64 .C................................................,..,..,.,,,^:a^:,^:t I%IIGIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIII7I0II#I% +chrM 794 C C 179 0 25 69 .$G$..A.............................................,..,..,.,,,,,g^:,^!.^:a^:,^:a I$:I3I4IIIIIIHIIIBIIIIII6IIII*IIIIIIIIIIIIIIIIIIII(II?II/IEII%I$II$$$ +chrM 795 T T 212 0 25 74 .$.$.$.$.$.$...A....................................N.,..,..,.,,,,,,,.,,,^:.^:,^:,^!.^:.^:,^:, II$IIIIII9I9@IIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII*IB$I#%#II$2$II:II4I +chrM 796 A A 187 0 25 71 ..........................................,..,..,.,,,g,g,.,,,.,,..,,^:,^:,^:, IIIA637IIIAII@IIIIIIIIIII3IIIIIIIIIIIIIIIIIIIIII6IIII%I%II%I8IIIIIIGI+* +chrM 797 C C 227 0 24 86 .$.........................................,..,..,.,,,,,,,.,,a.,,..,,,,,^:,^!.^!.^!.^!.^!.^:,^!.^!.^:,^:,^:.^:,^:.^:, III/-:CIIICIIGIIIIIIIIIII%IIIIIIIIIIIIIIII5IIIII/IIII/6-II%%$I/III.I%I11IIIIIIIIA.IIII +chrM 798 A A 241 0 24 94 .......C.................................,..,..,.,n,,,,,.,,,.,,..,,,,,,.....,.N,,.,.,^:,^:g^!.^:,^:,^:,^:.^:,^:, IA;57*9&BIGIIIIICIIII/@I;IIII<%%IIIIIIIIIIIIIIIIII"I$I#II%>?IIIIIIIII(IIIIIIII"IIIIIII*IIIIIIG +chrM 799 T T 238 0 23 101 .$.$.$......................................,..,..,.,,,,,,,.g,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,^:,^:,^!.^!.^!.^!.^:, IIII0III<IIICIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2I?I?III;I$7'II6IIIIBI'IIIIII>IIE:IIIII$II<FI;=IIIIIIG +chrM 800 T T 241 0 23 102 ....................................N.,..,..,.,,,,,g,.g,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,n,....,^!.^:,^:,^:, I27IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII4IAII%I(II$.,IFIIIII3>+IIIIII?III,IIIII$IIIDI;:"IIIIIGI0II +chrM 801 T T 240 0 23 105 ....................................C.a..,..,.,,,cn,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,^!.^:.^:, IBIIGIIIIIIIIIIIIIIIIIIIIIIIII7IIIII'I#II$II4IIID$"(II&1&IIIIIII>I$IIIIIIIIIIIIIII3&II@IIIDIIIIIIII$DIII; +chrM 802 T T 237 0 23 111 .$.$....................................,..,..,.,,,,,,,.,,,.,,..,,,,,,.....,.N,,.,.,,,.,,,.,,,,....,.,,,..,^!.^:,^:,^:,^:,^:, I@IIIIIIIIIIIIIIIIIIIIIIII6IIIIIIIIIII'IIIII3I<IBIIIII*4-IIIIIII@IIIIIIII:I"IDIII<3&IIIAIC<I:IIIIII%E0II4IHDEG@ +chrM 803 C C 235 0 23 115 ....................................,..,..,.a,,,,,,.g,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..a.,,,,,^:.^:.^:.^:,^!.^:, GDE;I@IIIH@IIIIIBIIIIIIII)*IFIII.IIIBIIIII$I&I$+7*II#(.I/ICI0I+II0IIII=IIII?IIII5#III4I,IIIIIIICI$5III,IBIIAIIIIII1 +chrM 804 T T 238 0 23 118 .$.$.$.$................................,..,..,.,,,,,,,.,,,.,,..,,,,,,.....,.N,,.,.,n,.,,,.,,,,....,.,,,..,.,,,,,...,.,^:.^:.^:, III@I2IGI=IIIIIIEIIIIIIII:5IIIIIIIIIIIIIII6<I?IEHFII'45IIIIIII=10CIIIIIII"IDIIIG"HIIIAI:BIIIIIIAI-2III7IIC?6CIIIIII/II +chrM 805 A A 237 0 23 121 .$.$..............................,..,..,.,,,c,c,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,n,....,.t,,..,.,,,,,N..,.,..,^:.^!.^:.^!.^!.^:,^:. 1IIEII3>I*II3EB,IIIII2%IIIIIIIIIIIIIII=I/3B%$$II&I<III?IIII5I>IIIIIIIIHFDIIIIIIIIIIIA"IIIIIII$<DIIDIFI@B;"IIIII$IEIIIIIII +chrM 806 C C 235 0 23 123 .$.$.$...........................,..,..a.,,,,,,,.a,a.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,T.a.,,,,,...,.,..,.....,.^!.^!.^:,^:. III?;HIIII)II4IIIIIDFIIIII'IIIIIIIII%IIIII%III#%+I;III6I%I2IIIIIIIII?@GIIIIIIII)I2IIIIIIIII&II$I0IIIIBCIIIII(IIIIIIII3%II%I +chrM 807 C C 248 0 22 124 .$..........................,..,..a.,,,,n,,.g,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,A.a.,,,,,...,.,T.,.....,...,.^!.^:.^:.^:. IAEIIIIIIIIIIIIIIIDIIIHIIII,IDIII)IIII$"(II$)%I?III2I+CIIIIIIIIIIIIIIIIIIIII0I1IIIIIIIII&;I(I(III52%IIIII(4I0IIIII+III4IIIII +chrM 808 C C 226 0 22 132 .$..............NN........N,..,..,.,,,,,,,.,aa.,,..,,a,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..a.,,,,,N..,.,..,.....,...,.....^:,^:,^:,^!.^!.^:,^!.^!.^:, IIIII;AIIIIIII.""I?IIIIII"=IIIII%II$I'I+II$)7I=IGIII%;IIIIIIIIIIAIIII=IIIII+I43IIIIIIII%IIII/IIII5;"IIII1IIIIIIII7III/IIIIID46II4II: +chrM 809 T T 242 0 22 134 .$.......................N,..,..,.,,,g,,,.,,,.,,..,,,,,,.....,..,,.,.,,n.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,C..,.....,,,..,..,^:,^:,^!. IIIIII:IIIIIII01II8I1'II"EI,III3IIII&I$II(.(IIFIIIIII+IIIIIIIII1,IIIBI"III5I34ICIIIIII/IIII?IICC53IIIHII>I2IIIIII:IIIIIIII91III1II5I4I +chrM 810 A A 243 0 22 144 .$.$......................,.C,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,C,.,,,.,,,.,,g,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.^:,^:.^:g^:,^:,^:,^!N^!N^:,^:,^:, HIII28IIIGII;III*I,II>IB62$2IIDDIIIIIIII&IIIIIIIIIIIIIII*IIIIIII$IIIII>IIIIIIIIIIIIII#IIIIIIIIIIIIIIIII>IIIIIHEI.IIIIIIIIIIIIIIIIIIII(I#III""GI9 +chrM 811 A A 236 0 22 145 ...........CC.........,..,..,.,n,,n,,.,,,.,,..,,,,,,.....,..,,.,.,,,C,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,^!.^:.^:. >I<0I:IIII@&&2I<I9III>IA3IIIB5I"II"III,IGIII8IIIIIIIFIFIIII+II:IIII9-IIIIII3I9:IIIIIIIIIIIIIIIII,+IIIIIIIIIIFIIIIIIIIIIIIIIIIIIII>I+I3IIIIIII*III +chrM 812 G G 233 0 22 149 .............N........,..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,n,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,.N,,,.,.,,,,NN,,,.NN^:,^:,^:,^:t II1:I+II0IIII"1>I/IIIIIIIIIIIIIIIIIIII+:)III7IIIII)IIB(:=II:IIIIIDIA<IIIIII"IIIIIII(IIIIIIIIIIIIIIIII0+IIIIIII7II%IIIII=IEIIII"6III#I+7E-"">@%I""C9;$ +chrM 813 A A 237 0 22 157 .$.....................,CC,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,...C.,...,.....,,,..,..,,,.,.,,,,..,,,...,,,c^:,^:,^!.^!.^!.^!.^:,^:, I6-5E*IIII:A@I+C5A=II<I&*IIIIFIIIIIIII(IIIII)IIIIIIIIIIIIIIIIIIIIIIICIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII4IICIIIIIIIIIIAIIIII?III&I$IIIIIII%III2IF$IIIIIIII +chrM 814 A A 246 0 22 162 .$.$.$.$.$................n..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,g,C,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,...C.,,,..,..,,,.,.,,,,NN,,,...,,,g,,....,,^!.^!.^:.^:.^:,^:, IH;AIIIII=II8IIII+III">*IIIAIDIII#III+IIIIIDIIIIIIIIIIIIIIIHHHIII$I0IIIIIIIII=IIII#IIIIIIIIIIIIIIIIII?IIIIIIIIIIIIII%I;CIIIDIIII@I(I7III""38FIIIIF1+IIIIIIIIIIIIII +chrM 815 C C 246 0 22 160 .$.$..............,..,..,.,,,,,,,.,,a.,,..,,,,,,.....,..,,.,.,,t.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,a....,,....,a^:.^:.^:, IIIIIIIIIIIIII:IIIIIII8IHIII$III*6=IIIIIII@I*IIIEI8IIIIIIIIII-IIIII:IIIIIIIII$IIII<IIIIIIIIIII2IIIIIIICIEIIIIIIII/I2IIIIIAIII*I#I2$IIII*III8C5$9$IIII9/IIII<&II8 +chrM 816 A A 255 0 22 169 ..............,.C,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,.NN,,,g,,....,,....,,..,^:,^:,^:.^:,^:,^:.^:.^:,^:,^:,^!. IHEF8II?+GI:I@I7%IIIIAIIII+IIA'II>II@IIIIIII3IIIII/III7IIIII5IIIIIIIIIIIIII+IIIIIIIIIIIIIIIAI6IIIIII;I8IIIIIIIIIIFIIIIIIIIIIIIIIIIIIIII""IIIAIIIIIIIIIIIIIIIIIIIIIIIIIIII +chrM 817 A A 254 0 22 171 .$.C.......T..Nn..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,n,N,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,.^:.^!. IDIII?9=<0$I2"":I*III1IIIIIIII.I@FII5IIIIIIII322+IIIII3III"I"IIIGIIII2>IIIIIIIIIIIIIIIIIF4IIIIIIIII)-I>IIIIII>IIIIIIIIIIIIIIIIIIIIIII6IIIIII$IIIIIII?IIIIIIIIIIIIIIIIIIIIII +chrM 818 G G 239 0 22 174 .$.$.$.$........N,..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,.NN,,,n,,....,,....,,..,,,.,,..,,,...^:,^:,^:.^:, IIIII<I>?*I4"II&II4IIIIII8III3I3IIIIIIIIIIIIII=5IIIIIIIIIII<IIIIIIIII<IIIIIIICIIIIIIIIIIIIII?IIIIIIII%IIIIIIIIIIFIIIII9III&IIII3II:=II""ID;"IIIIIII5IIIIIIIIII:II7IIIIIIII-III +chrM 819 A A 244 0 22 177 .$........,.C,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,^:.^:.^:,^:,^:,^:.^:. I.;4I%765I5$IIII+IIIIIIIAIII7II3IIIIIIIFIII%IIIII1IIIII:III9IIII1,I7IIIIIIIIIIIIII(I9IAI)III>II+III8IIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIII'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII7IIIIIIIII +chrM 820 A A 255 0 22 183 .$.......,..,..,.,,,,,,,.,,,.,,..,,,,,,....C,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,...C.,...t.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.g,..,,,...,g.,..,,,..^!.^:.^:.^:.^:,^:,^:, I3/I+:DII7&I&I*<III$$(II;II@II2IIIIIIIIIII&IIIIE2IHIII)IIIDIIIIDCI>/BIHIIIIIIIIIIII'III6IGIII+7IIII@IIIIIIEIIIDIIFI9IIIIII9II1,+III.I(83IIIII4GIIIIIIIIIIBI,BIIIIIIIII$IIII<5@IIIIIII9I +chrM 821 C C 246 0 22 188 .$.$.$....,..,..,.,,,,,,,.,,,.,,..,,,,a,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.n,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,^:,^!.^:,^:,^:,^:. ?I,0IIIIIIIIIC1III&I.II%IIIIIIIIIII'IIIII3IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIIIIIIIAIII/IIIIIIII3I,IIIIIIII?IIIIIIIIIII"IIIIIII<IIIIIF$IIIIIIIIIIIII&IIIIIIIIIIIIIIIIIIIIIII-7IIIIIIH/I&IIIII +chrM 822 T T 242 0 22 186 .$.$.$.,..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,N,,..,,,...,,.,..,,,......,,,,.,,,.^:, &IIIII%IIII3III%I$II)/IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIII4I'IIIIIII0IIIGEI-IIIII:II,IIIIIIIIIIIIIIII3I@IIIIIFIIIII&IIIC1I*0IIIII03IIIIIIII=8>"D3III;IIIIEIIAII-2+IIIIII0@20I369II +chrM 823 T T 252 0 22 192 .$,$..,..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,c,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,n,,..,,,...,,,g,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,^:.^!.^:,^:,^:,^:,^:,^:,^:, IIIIIII79I0IIIIII$&>IIIEIIIIIAIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEII$IIIIEEIIIIIIII4IIIIIIII'IIIIIIII(;III;IICI@I+II"<CII>=/III6:B#0IIIII0FIIIIDIII5E6I@8IIIIGIII9II=II.$)IIIIII9>0:I59BIIII/E2?BA/ +chrM 824 T T 244 0 22 196 .$.$,$..,.,,,,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,N,,..,,,...,n.,..,,,......,,,,.,,,.n..,,,,,,,^:.^:,^:.^:,^!.^:, IIIIII=IIIIIIII,4IIIIIIIIIIIIIIII<IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEIII9?0&IIIIIIIII>CIIII3II/IIICIIICII:I+III;I6DII27FIIII;:%1IIIII11IIII>III75:"I;IIII>III;"IBII232IIIIII+;56I5/<I"II(76?@B-I@I-I> +chrM 825 A A 252 0 22 196 .$.,.,,,,,,,.,,,.,,..,g,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,^:,^:n^:, IIIIIIIIIIIIIII:II0II&IIII@C4I7I:IIIIIIIII<III8IIII3,I8IIIII=IIIIIIIIIIIIII6IIIHII)I4IIIIB>I9IIIIIIIIIIIIIIIIIIIIIIII**IIIIIIIII0IIIIIIIIIIIII*IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIII9IIIIIIIIIIIII"I +chrM 826 A A 255 0 22 198 .$,$.,,,,,,,.,,,.,,..,c,,,,....C,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,C.,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.g..,,,,,,,.,.,.,,,g^!.^:.^:, IIIIIIIIIIIIII=II4II#IIIIIIII'IAIIIFIIIIIIIIIFIIII40IIIIIII/IIIIIIII8IIIII'I@III4II/IIIIIIIIIIIIIIIIIICI#IIIIF%#II)IIIIADIGIIIIIIIIIIIIIIIIIII%AIIIIIIIIIIIII/337II@IIII/I:IFIII#II/BI9I;EIIIEIIII@III +chrM 827 C C 253 0 22 200 .$,$,$,$,,,,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,N.,.,,,,,...,.,T.,.....,A..,.....,,,..,..,,,.,.a,,,..,,,...,,,,,,....,,....,,..,,,N,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,^:.^:.^:.^!. IIIIIIIIIIIIIII8IIIIIIIIIII*IIIIIIIIIIIIIIIIIIFIIIIIII+II"IIIIIIIIIIIIII%IIIII<II$IIIIIIIIIIIIIIIIIIIIII)IIIIIIIIIIIGIIIIIIIIIIIIIIII&IIIII"IIIIIIIIIIII"IIII=DII+IIII8IIIIIIIIII;8I0II?IIIIIICIIIIIIIII +chrM 828 C C 255 0 22 199 ,$,$,$,.,,,.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,g...,,,,,,....,,....,,..,,,.,,..,,,...,,N,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....^:,^:,^:, IIIIIIIIIII8IIIIIII7IIIIIIIIIIIIIIIEIIIFIIIIIIIIII$IIIIIIIIIIIEIIIII&IIIII;@I-IIIII<IIIIIIIIIIIIIIIIIIIIIIII'IIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIB"IIIIIIII*IIIH9IIICIIIIIIF/I8I<@IIIIIII>IIIIIIII(%I +chrM 829 C C 249 0 22 197 ,$.$,$,$,$.,,..,,,,,,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,t,,....,,....,,..,,,.,,..,,,...,t.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,^:, IIIIIIIIIIIIIIIIID6.;IIIIIIIII(IIIIIIIIIIEIIIII&IIIIIIIIIIIIIIIEI&IIIIIE-I9II8IIIIIIIIIIII=IIII?IIIIIIIIIIIIIIII#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII%IIIIIH+IIIIII#2I9III@IIIIIAI0ICIIIIFIII=<IIIIIIIA*I: +chrM 830 G G 255 0 22 198 .$,$a$.$.$,$,$,,,,.NNNN,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,C..,...C.,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,^:.^!.^:c^!.^:,^:, <II1IIIIIIIA""""I0III;IIIIIIIII=IIIIC<IIIIIIIIIIIIIIIIII.III3<IIIIIII)IIIIIF%)IIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIHIIIIIIIII9III=IFIIIIIIIIBIIIIIIIIII:IIIIIIIII:III8III9IIIIIII7II#IBI +chrM 831 G G 255 0 22 195 ,$,$,$,.....,..,,.,.,,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,..C,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,T,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,^:.^:.^:.^:. IIIIE?B,,IIIII3IFIIIIIII;IIII>7@>IIIIIIIIIIIIIIIIIIBII@IIII$2I1I/IIII:IIIIIIIIIIIIIIIIIIIIIII5IIIIIIIIIIIIIIIIICIIIIIIIEIIIIIIIIIIIIIIII9IIIIIIIIII%II/<IIIIIIIIIIIIEIII<IIIDIIIIIIIIII@4II&IBIIIII +chrM 832 A A 248 0 22 195 ,$N$.$.$.$.$,$.$.$,$,$.$,$.$,$,,.,,,.,,,,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,t...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,....^:.^:.^:, I"I,G>I(III+I0IIIHIII2IIII49+*I8IIII9I>IIIIIH;(I>I4HI5>GHII&IIIIA?IIIIIIIIIHIIIAIIIIIIIIII'II>IIIIII?I<EIIDE5III5IIIIIIIIIIII9IIIIIIIID;BHI3IIEI'IIIDI:IIII4I8I;IEIIIIII1-BII@IIIDIII;II$IIIIIIIII: +chrM 833 C C 247 0 22 185 ,$,$.$,$,$,$.$,$,$n,....,.,,,..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,g,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,^!.^!.^:n^:n^:, IIIIIIHII"II?IIIIIIIIIIIIIIIIIIIIII=I'III0HI-IDIIIIIIIIIIIIIIIIII0IIIIIIIIIEIIIIIIIIIIIIIICIIIIIIIIIIIIIIIIIIII&IIIIII(II>IIIIIII$IIIIIIIIII<II7IIAIIIIII-I?IIIIIII(.;+II)I2IIIIIII1II""6 +chrM 834 G G 247 0 22 181 ,$,$.$.$.$.$,$.,,,..,.,,,,,...,.,..,.....,C..,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,^!.^:.^:,^:,^:. II5,IEI8IIIIIIIIIIIII8FIII+IIIFI99I$I'III@>:IIIIII@IIIIIIIIIIIIIII6IIIIIIIIIHIH:IIIIBIIIIIIIIIIIIIIIIIIIIIHI=-IIIIIIIIII/IIIIIIIIIIIIIIIIIIIIAIII7=II?IIIIIII?II%I1IIIIIIIIIIIIIIIIII +chrM 835 A A 247 0 22 178 .$,$,$,$..,.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,g.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.^:,^:.^:,^:, IIIIIII9IIIIIIF+I2IE4I<7I.'I%>III>4I5IIIIIIIIIIIIIIIIIIIIII@IIIIIIIII@)@IIII>IIIII<IIIIIIFIIIII4II#II7+IIIDI<IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII$IIIIIIIIIIIIIIIIIIIICIII +chrM 836 A A 255 0 22 176 .$.$,$.,,,,,...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......n,,,.,,,.,..,,,,,,,.,.,.,n,,..,....,,,,..,.,,......,..,,,..,,.,.,,^:,^:. IHIDIIIII(a)G4III96II1I*.I)I*I8-IEIIIIIIIA;IIIAIIIIIIIIIIIIIIIIIIII2I2&II>A2IIIIIIIIC=IIIIIIHIIIIEIHIIII<=FIII"IIIIIIIIIII9IIIIIIIIIIII"IIIFIII'IIIIIIIIIIIIIIIIIIIIII;IIIIIIIIIII +chrM 837 A A 253 0 22 174 .$,$,$,$,$,$...,.,..,.....,...,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,T,.C,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,.^!. IIIIII5EIIFIIEII2I/EI1CIIIII9IIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIAIADIIIF?IIIIEIIIIIIIIIIIIIIII#I=&IIIIIBIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<IIIIIIIIIIII/IIIIIIIIIIIII=IIIII@IIIDII +chrM 838 G G 255 0 22 169 .$.$.$,$.$,$..,.....,A..,.....,,,..,..,,,.,.,,,,..,,t...,,,,,,....,,....,,..,,,.,,..,,,.C.,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,n,,..,....,,,,..a.,,......,..,,,..,,.,.,,,..^!. AIEIII;>IIFI<?I,FIII8I)IIII*1IIIIIIIIIIIIIIIII9IIIIIIIIIGDG;IIIIIIIIIIIIIIIIIIIIII%IIIEIE6IIIIIIIIIIIIIIAIIIIIIIIIIIIIIIIHII"@IIIIIIIIDI%@II#IIIIIIIIIGIIIIIIIIII5IIF:III +chrM 839 T T 247 0 22 170 .$N$,$.....,A..,.....,,,..,.N,,,.,.,,,,..,,,...,,,,,,....,,...C,,..,,,.,,..,,,.N.,,A,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,...^!.^!.^!.^:,^:.^:.^:, 2"IA4I&)I%BII43,46IIIIIID"IIIHIII:IIIIIIIIII+IIIII2-20II=<&,IIIIIIIIIIAIIIIA"III3I2.DAC9I$IIIIIIII?:IIII<:IB=IDIIEI<I>IA?I44IDI<2IC5II-II7IIIIII:IIII9II**I3IB;4IIIIII1IIG +chrM 840 C C 243 0 22 173 .$.$.$.$.$,$.$..,.....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.a,......,..,,,..,,.,.,,,......,..,^:.^!.^:.^:.^:,^:, III->I+IIIIGI-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII?IIIIGIIIIIIIIIIIIIIIIIIEAII)/IG78I%@I.IIIIIIIIIIIIIII@IIIIIIHIIIIIIIIIIIIIIIIII8II&$%IIIIIII@III&IIICC&CIIIAIIIIII:IIIIIII64 +chrM 841 T T 255 0 22 174 .$.$,$.$....,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,^:.^:.^:.^!.^:.^:.^:.^:. BIIII,IIIIIIII8IIIIIIIIIIIIIIIIIIIIIIIII8?9EIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII;FI$IIIIIIIIIIIIIIG3AFIII0III:I6IIIII3IIIIIII5II9I;0IIIIII@III&5II>>%5I>I-IIIIIIIIIIIIII1*IIIIIIII +chrM 842 C C 239 0 22 173 .$.$.$.$,,,..,..,,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,.T.,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....aa,,..,.,,......,..,,,..,,.,.,,,..A...,..,....,,..N.....^:a^:.^!. IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC5CIIIIIIIIIIIIIIIIIIIIIII#II%+II5IIIIIIIIII-IIIIIII<IIIIIEIII4IIIII:IIIIIIIII-II>II$I*IIIIIIIIIIIIIII10$7I<BDII&III>IIIIIII0'II"IIIII&II +chrM 843 C C 246 0 22 175 ,$,$,$.$.$,$.$.$,$,,.,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,N,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,..A...,..,....,,........,..^:.^:.^:.^!.^:.^:, IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEICBIIIIIIIIIIIII+IIIIIIII;III+II:IIIGI*IIIIEIIIIIIIIIIIIIIIII"IIIII=IIIIII>IIIII0II&IIII+IIII@IIIIIIIIII3II>5II$IIIBIIIIIII.<IIIIIIII#IIIIIII: +chrM 844 A A 255 0 23 169 ,$,$.$,.,,,,..,,,...,,,,,,....,,....,,..,,,.,,..,,,...,n.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,.......,^:.^:.^:. II8IIIIII47IIIFIIIIIIII17,.II9B.9III4IIIEII2AIII/+II"%I8GIII(69?=<IIII;IIIIII;IIIIIIIIIIIIIIIIIIIIIIIIIIIIII@III2IIIBIIIIIIFIIII?IIIHIIIIIIIIIIIIII91IIIIIIII4IIIIIII9III +chrM 845 T T 246 0 23 166 ,$.$,$,$,$,$.$.$,$,$,$...,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,n,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,.......,... IIIIIIIIIIIIIIIIIIII745BIICAEIIIEIIIIIIIIIIII@CIIIIID2H?HIH+IIIIIIIIIIIII9I@9IIIIFIIIIII"IIIIIIIIII4IIII(IIIIIIIIIEIIII-IIIII4IF6/IIIIII<IIIIIII+:IIIIIIII%IIIIIII-III +chrM 846 G G 255 0 22 157 .$.$.$,,,,,,....,,....,,..,,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,.......,...^!.^:, IIIIIIIII:?04IIHI;IIIIIIIII&IHIIIIC&IIIIII5IIIG>@EIFIIIIIIIIIIIIIIIIIIIDIIIIIIII@IIIIIIIIIIII%EIIIIIIIIIIIIIIIIIIIIIII?IIIIIIIIIIIIII@IIIIIIIII&IIIIIII=IIII0 +chrM 847 A A 243 0 23 159 ,$,$,$,$,,....,,....,,..,,,.,,..,,,.N.,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......n..,....,,....N.N.,.......,....,^:.^:.^:.^:.^:c IIIIII/+,.II4,3III9EIII=II6DIII+"III@I=$IIIA6)IIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIII6-1IIIIIIIIIII4I9IIIIIIIIIIIIIIIIIIIIIIII"IIIIIIIIIIIII"I"I+IIIIIII@IIIIIIIII, +chrM 848 A A 245 0 23 158 ,$,$.$.$.$.$,$,$....,,..,,,T,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,.......,....,....,^:.^:.^:, II0341II4-E5II=IIII#II1IIIIB&BII-IIIIII1B,II1IIII5IIIII>IIIIIIIIIIIIIIIIIIIIIIIBIIIIIII4IIIHI6IIIIIIIIIIIFIIIIIIIIIIIFIIIIIIII6IIICIIIII9IIIIIIIF8I.IIIIII=III +chrM 849 A A 244 0 23 150 .$.$.$.$,$,$..,,,.,,..,,,.C.,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,..C.,,,,..,.,,......,..,g,..,,.,.,,,......,..,....,,........,.......,....,....,.., .?><IIH3III1II48III4$IIIBI=IIII92*II;IIIIIGIIIIIEIIIIIIIIIIIIIIIIIII<@(:IIIIHI?IIII+IIIIIIB&&EII<>I8II+>IIIIIIIIIIIIII$<IIIIII,I/IIIIIII2IIII0IIII'IIH +chrM 850 C C 245 0 23 146 .$.$,$,,.,,..,,,...,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....g,....N.N.,.......,....,....,..,^!.^:. <;IIIIIIIBIII3I;IIII;8III,B%I8/IIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIG5=IIIIII5I+II0IBIIIIIIIIIIIIIIIIIIBIIIIIIIIIIIII$IIIII"I"IIIII(&IIIIIII7IIII2IIIII +chrM 851 T T 238 0 23 145 ,$,$.$,$,$.$.$,$,$,$.$..,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,g,..,,.,.,,,......,..,....,,........,.......,....g....,..,..^:,^:. IIIIIBEIII:3III2I<(I$I9@2IIIAIIIIIIIIII9+IIIIIIIIIIIIIEII7/IIIII%IIII+7III>IIIICIII,;IIIII+IC(,IIIIII7IIIIIII(:IIIIIIGIBIIIIIII+IIII.IIII'II+II+I +chrM 852 G G 240 0 23 135 .$.$,,.,..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,a,..,,.,.,,,......,..,....,,........,.......,....,....,..,..,.^:. IDII>I>$III:3%DIII4II.IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG&%IIIIIIIIIII=IIIIIIIIIIIII#BIIIIIIIIIIIIIIIIIIIIIII&I5IIIIIIIII +chrM 853 G G 254 0 23 140 ,$,$.$,$..,,,......,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........c.......,....,....,..,..,..^:.^:.^:.^:.^:.^:.^:. II<IC=III78(CIIIIIIIIIIBII?IIIIIIIIIIIIIIIIIIIIHI6IIIIIIIEIIIIIIIIIIIIIIIIII$IIIIIIIIIII3IFIIIIII@IIII:I+I1IIIIIIIAIIIIII+I3IIIIII1IIIIIIIII +chrM 854 A A 254 0 23 137 .$.$,$,$,$.$.$....,,,,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,n..,,.,.,,,......,..,....,,........,.......,....,....,..,..,.........^:. :%III;1&6*+IIII8IIIII4BIIIIIIIII7IIIIIIEFIBI+>IIIIH6I<III2EI67IIDII"IIII%IIIIIIIIIIDIIIIII@EIIIIII*I%IIIIIIIII;IIIIIIIIG+IIIII0IIIIIIIIII +chrM 855 G G 246 0 23 133 .$.$.$.$,$,$,$,.,,,.,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,C,.,,,......,..,....,,........,.......,....,.T.T,..n..,..........^:.^!,^:. +II8IIIIIIIIII=IIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIII<=AIDIIIIIIIIII#IIIIIIIIIIIIIIIIIII%I+II8IIAIIIIIIIIIIIIIIII%I1III"IIIIIIIIIIIIIIEI +chrM 856 A A 239 0 23 128 ,$N$,$,$,$.$,..,,,,,,,.,.,.,,,,..,....,,,,..,.,,......,..,,,..g,.,.,,,......,..,....,,........,.......,....,....,..,..,...........,.^:.^:. I"III;I;IIIIIIIIIIAIIIIIIIIID(a)3+IIII??I;III.4&I;IIIIIIII->DI:IIIIIII5GIIEII?GI-IIIII*I3I3II2III?EIIIIIIIII+IIIIIIIIIIIIIIIII3III +chrM 857 C C 254 0 23 124 ,$..,,,,,,,.,.,.,,,,..,....,,g,..,.,,......,..,,,..,,.,.,,,......,..,....,,........a.......,....,....,..,..,...........,...^:.^:. I06IIIIIIIIICIIIIIIIIIIIIIII#IHIIIIII3IDI9IHI+$IIIII#IIIII>IIIIIIIIIIIII#=IIII8I5IFIIIIIIIIIIIIDIIII/IIDII>IIIIIIIIIII1IIIII +chrM 858 T T 240 0 23 125 .$.$,$,$,$,$,$,$,$.,.,.,,,,..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,......N,....,....,..,..,...........,.....^:.^:. .:IIIIIIIIIIIIIIIII7IIII4IIIIII9.III5IIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIII<2DIIIIIII4IIIIII"=IIIIIIIIIIII;II4IIIIIIIIIII-IIIIIII +chrM 859 A A 250 0 23 118 .$,$.$,$.$,$,,g..,....,,,,..,.,,......,..,,,..,,T,.,,,......,..,....,,........,.......,....,....,..g..,...........,.......^:.^:. II9IIIIII@DIC=.EIIIIE@IIIII*CI8-IB8IIIIIII$IHIIIIIIIIIIICIHIIIIIIIIIII@IIIIIHIIIFIIIIIIFI-III*III)IIIIIIIIIIIIIIIIIIII +chrM 860 A A 255 0 23 115 ,$,$,$..,....,,,,..,.,,......,..,,,..,,.,.,,,......,..,....c,........,.......,N.N.,....,..,..,..G........,........C^:.^:.^:. IIII2IEA(IIIIIHAIIIIG,=G1,IIIIII:EIIII6IIIIIII@IIIIIIIIIEIC@43:I,I@IIIIIIII"I"IIIIIIAIIIIIII*4IIIIEEIIIIIIIIIII%III +chrM 861 A A 235 0 23 115 .$.$,$....,,,,..,.,,......,..,,,..,,C,.,,,......,..,....,,........,.......,....,....,..,..,...........,............^:.^:.^!, E4IB+I(IIII85IIIII&5&43IIIIII@III(I+IIIGIIIIHIA:IIIIIIIFIII$I+3IIIIIIIIFIIIIII@I6IIIIIIII8IIIIIIIIIIIIIIIIIIIIIIIII +chrM 862 G G 235 0 23 115 .$.$.$.$,,,,..,.,,......,..,,,..,,.,.,,,......,..,....,,........,.......,....,.T..,..,..,...........,..............,^:.^:.^:. IIIHIIIIIIIIIII1III>IIIIIIIIII&IIIII-IIIIIIIIIIIII+I7III+I1I&IIIIIIIIIIIIII-I+IIIIIIIIIIIIIIIIIIIIIIII?IIIIIIIIIIII +chrM 863 G G 243 0 23 115 ,$,$,$,..,.,,......,..,,n..,,.,.,,,......,..,....,,..N.N.C.,.......,..C.,....,..,..,...........,..............,...^:.^:.^:.^:. IIII?IIIIII%III<IIIII"IIII:I=III5IIIIIIIIIIIIIIIFI"I"I.IIIIIIIIII#I%III&I'IIIIII.IIIIIIIIIIIIIIII4IIIIIIIIIIIIIIIII +chrM 864 A A 230 0 23 114 ,$..,.,,......,..,,c..,,.,.,,,......,..,....,,........,.......,....,....,..,..,...........,.........N....,.......^:.^:. I53I;III#<'*.II0II#7)II%IIIII0III;II9II64IIII0I)I:EIE&III0IIII3I7III:I:IIIII7IIIIIIIB;IIIIIIIIIIIII"IIIIIIIIIIIIII +chrM 865 G G 255 0 23 115 .$.$,$.$,$,$......,..,,,..,,.,.,,,......,..,....,,........,......N,....,...T,..,..,..........A,..............,.........^:.^!, IDIIIII6IIIIIIIIIIIIII9IAIIIIIIIIIIIIIIIII7IIIIIIIIIIIIIIII"IIIIIII,I1IIIIIIII+IEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII3 +chrM 866 G G 230 0 23 109 .$.$.$.$..,..,,,..,,.,.,,,......,..,....,,........t.......,....,....,..,..,...........,..............,.........., G:IIB?IIIIIIIIII%IIIII,IIIIHIIIIIIII/IIIII0I(I&IIII.IIIIIIIII'I,IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII)IIIIIIIIII3 +chrM 867 A A 224 0 23 105 .$.$,$..,,,..,,T,.,,,......,..,....,,........,......N,....,....c.N,..,.CC........,..............,.........., .'IG4III/III$IFIII3III&;I@CII160II99II.G%GIFI:)ID"IHIIIIF,F*II"II;II$%+B0I/-A.IHIIIIIIIIIIIIIIIIIIIIIIIII +chrM 868 T T 248 0 23 102 .$.$,$,$,$..,,.,.,,,......,..,....,,........,.......,....,....,..,..,...........,..............,.........., IIIIIIIII#IIIIIIIIIIIIIIIIFIIIIIIIIIICIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII(@IIIIIIIIIIIIIIIIIIIIIIIII= +chrM 869 T T 225 0 23 101 .$.$,$,$.$,.,,,......,..,....,,........,.......,....,....,..,..,...........,..............,..........,^:N^!,^:.^:. IIII%I=IIIIIIIIIIIIIIIIIHIIIIIIIII%III>IIIIIIIIII>I1IIIIIIII:IIIIIIIII?IIIIIIIIIIIIIIDIIIIIIIIII3"$II +chrM 870 T T 228 0 23 99 ,$.$,$,$,......,..,....,,..N.....,.......,....,....,..,..,...........,..............,..........,.,.C^:.^:.^:A I*IIIIIIIIIIIIIIIIIII2I"I%I%IIII@AII$IIIIIII0I+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII,I(I+II$ +chrM 871 A A 208 0 23 97 ,$.$.....n.C,....,,........,.......,....,....,..,..,...........,..............,..........,N,.....^:.^:. I;III1I"F%I8II<II5FI6.I8IIIIGIII7IIIIIII+G+IIIIIIII7IIIIIG<IIIIIIIIIIIIIIIIIIIIIIIIIIIII"(IIII&II +chrM 872 G G 211 0 23 95 .$....,..,....,,........,.......,....,.T..,..,..,C..........,..............,..........,.t....... III65II-IGIIIIIAIIBCI*IIIIIIIIIIIIIIII$I&IIIIIID#IICI*IIIIIIIIIIIIIIIIIIIIIIIII&IIIIIII$IIIIIII +chrM 873 C C 206 0 23 94 .$...,..,....,,........,.......,N.N.a....,..,..,...........,..............,....N.....,.g....T.. II9EII9IFIIIIIIII/EIBIIII?GIIII"I"III/I-IIIIIIIIBIIIIIIIIIIHIIIIIIIIIIIIIIIIII"IIIII?+$IIII$II +chrM 874 A A 208 0 23 94 .$.$.$,$.$.$,$....,,......C.,.......,....,....c..,..,...........,.....N........,..........,.g.......^:. II<IA&IIEIIII9DII(I&IIGI63IIIIIIIIII.I/II&IIIIIBII(a)5I3.II)IIIII"IIIFIGIIIIIIIIIIII1II)IIIIIIII +chrM 875 G G 210 0 24 87 .$.$.$.$,$,$..N...C.,.......,....,.T.T,..,..,...........,.........N....,..........c.,........ BIIIII:I"I$I%IIIIIIIIIIIIIIII'I$IIIIIIII%I;IIIIIIIIIIIIIIIII"IIIIIIIIIIIIIII$I+IIIIIIII +chrM 876 T T 191 0 24 81 .$.$.$A$.$.$.$.$,.......,C...,....,..,..,..........C,.........N....,..........,.,........ $II$(I.=IIC3-2IFI#I$II>IBIIIIIIIII.$IIII2=I+IIIIIIIIII"IIIIIIIIIIIIII>'IEIIII-III +chrM 877 A A 203 0 24 73 ,$.$.$.....,....,....,..,..,...........,..............,..........,.,........ IIII*:IIII=IIII1I%IIIIIIIIIIIIIII8IIIBIIII'IIIIIIIIIIIII$HIIIIIIIIIIIIIII +chrM 878 A A 195 0 24 70 .$.$.$.$.$,$....,....,..,..,...........,..............,..........n.,........ I>IIII?IHIIA,A+II>IIIII=IIEIG(0ICIC?IGIIIIIIIIFIIIIIIIIIII6"IIIIIIHIII +chrM 879 A A 155 0 24 64 .$.$.$.,....,..,..g...........,..........NN..,..........,.,........ IIIDI3<3BIIII@I#II:IC4@;13IIIIII9IIIII""BIIIIIIII4II6IIIIIIIIIII +chrM 880 T T 172 0 24 61 .,....,..,..,...........,..............,..........,.n........ IIIIIIIIIIIIIIII2IIIFEIIIIIIIIIIIIIIIIIIIIIIIIIIII<I"IIIIIIII +chrM 881 T T 188 0 24 61 .$,$....,..,..,...........,..............,..........,.,........ II9:=+IIIIIIIII;IIIIIII,IIIIIIIIIIIIIIIIIIIIIIIIII-I+IIIIIIII +chrM 882 A A 155 0 24 59 .$.$.$.$,$..,..,...........,..............,.....N....,.t.......N C(B(IIDIIIII5II26-A@/III>I?I=8I9II0F=IIIII$"5III%I$IIIICII" +chrM 883 A A 161 0 24 54 .$.$,$..,...........,..............,...N......,.,........ IIIIII5I8GH%AIIIIII<IIII=BFIII=IIIII"-I3IIIII#GIIIIIII +chrM 884 G G 136 0 24 51 ..,T..........,..............,...N......,.,........ 8II//IHI?IIII;IIIIIIIIIIIIIIIIIII"IIAIII'IIIIIIIIII +chrM 885 A A 127 0 24 52 .$.$,...........,..............,..........,G,........^:. IIII@2:?IBIIIIII9IIIDIIBIIIHIIII>II45II>I$I7III&IIII +chrM 886 A A 145 0 24 50 ,$.$..........,..............,..........,.,......... II8;IB&A<81*II3IIIIII@IIIIIIEIIII66IIII:'@III/IIII +chrM 887 T T 107 0 24 48 .$.........,.....N........,..........,.,.......N. IIII@I76IIIIIIII"IIIIIIG0IIIIIIIIIIIIIIIIIIIII"I +chrM 888 A A 126 0 24 48 .$.$.$.$.$.$.$..,..............,..........,.,.........^!, IIC;EIID&IAAICIIIIIIIIIIIIG;I*I/IIA7II<III:II$II +chrM 889 G G 133 0 23 41 .$.,..............,..........,.,........., I=II9IEIIIHBIIIIII@IBIIII5ICIIIICI-=IIIII +chrM 890 A A 132 0 23 40 .$n$.$.............,..........,.,........., 6"I?IDI(GA6I=IFIIIIIIIIFII/III=III%IIFII +chrM 891 G G 119 0 24 38 .$.$......N....,..........,.,...T.....,^:. 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III.I.I=II:I0DI4I?I6IDIIIIIIIDIIIIIIII1IGIIIIIII<IIII%IIIIIIIIIIIIIIIIII>I1IIIEIIII6I#IIII2I"IIIII$IIIIIIIIIGIII"IIIIIIII:H8I +chrM 978 T T 235 0 23 123 ,$,$A,..,.,..,........,,,.,,.,,,,,..,,....,,,...,,.......,..,..,NN,.,,,...,,..,,,......,..A,,,.,,,,,,,.,.,.,,.,,,,,,....,,,.^:. 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IIIII 0 0 0 0 5 +chrM 449 G 6 ,,,..^:, IIIII6 0 0 0 0 6 +chrM 450 A 6 ,,,.., IIIIII 0 0 0 0 6 +chrM 451 A 6 ,$,,.., IIIIII 0 0 0 0 6 +chrM 452 A 5 ,,.., IIIII 0 0 0 0 5 +chrM 453 G 5 ,,.., IIIII 0 0 0 0 5 +chrM 454 T 6 ,,..,^:, IIIIII 0 0 0 0 6 +chrM 455 G 6 ,,..,, IIIIII 0 0 0 0 6 +chrM 456 A 6 ,,..,, IIIIII 0 0 0 0 6 +chrM 457 C 6 ,,..,, IIIII= 0 0 0 0 6 +chrM 458 T 6 ,$,..,, IIIIII 0 0 0 0 6 +chrM 459 T 5 ,..,, IIIII 0 0 0 0 5 +chrM 460 T 5 ,..,, IIIII 0 0 0 0 5 +chrM 461 A 5 ,$..,, IIIII 0 0 0 0 5 +chrM 462 A 4 ..,, IIII 0 0 0 0 4 +chrM 463 T 4 ..,, IIIC 0 0 0 0 4 +chrM 464 A 4 ..,, IIII 0 0 0 0 4 +chrM 465 C 4 ..,, IIII 0 0 0 0 4 +chrM 466 C 4 ..,, IIII 0 0 0 0 4 +chrM 467 T 4 ..,, II>? 0 0 0 0 4 +chrM 468 C 4 ..,, IIII 0 0 0 0 4 +chrM 469 T 4 ..,, IIIG 0 0 0 0 4 +chrM 470 G 4 ..,, %III 0 0 0 0 3 +chrM 471 A 4 ..,, 4;II 0 0 0 0 3 +chrM 472 C 4 ..,, II3I 0 0 0 0 3 +chrM 473 T 4 ..,, IIII 0 0 0 0 4 +chrM 474 A 4 ..,, ;III 0 0 0 0 4 +chrM 475 C 4 ..,, IIII 0 0 0 0 4 +chrM 476 A 4 .$.$,, 32II 0 0 0 0 2 +chrM 480 T 3 ,,^:. III 0 0 0 0 3 +chrM 481 A 3 ,,. III 0 0 0 0 3 +chrM 482 G 3 ,,. III 0 0 0 0 3 +chrM 483 C 4 ,,.^:, IIIE 0 0 0 0 4 +chrM 484 T 4 ,$,., III9 0 0 0 0 4 +chrM 485 A 3 ,., III 0 0 0 0 3 +chrM 486 A 3 ,., III 0 0 0 0 3 +chrM 487 G 3 ,., III 0 0 0 0 3 +chrM 488 A 3 ,., III 0 0 0 0 3 +chrM 489 C 3 ,$., III 0 0 0 0 3 +chrM 510 C 3 .,^:. III 0 0 0 0 3 +chrM 511 C 3 .,. III 0 0 0 0 3 +chrM 512 A 3 .,. 6II 0 0 0 0 3 +chrM 513 C 3 .,. III 0 0 0 0 3 +chrM 514 T 3 .,. III 0 0 0 0 3 +chrM 515 A 3 .$,. III 0 0 0 0 3 +chrM 518 C 3 ,$.^:. III 0 0 0 0 3 +chrM 520 T 3 ..^:, III 0 0 0 0 3 +chrM 521 A 3 .., III 0 0 0 0 3 +chrM 522 G 3 .., II, 0 0 0 0 2 +chrM 523 C 3 .., III 0 0 0 0 3 +chrM 524 C 3 .., II7 0 0 0 0 3 +chrM 525 C 3 .., III 0 0 0 0 3 +chrM 526 T 3 .., II? 0 0 0 0 3 +chrM 527 A 3 .., III 0 0 0 0 3 +chrM 528 A 3 .., III 0 0 0 0 3 +chrM 529 A 3 .., FII 0 0 0 0 3 +chrM 530 C 3 .., II+ 0 0 0 0 2 +chrM 531 T 3 .., III 0 0 0 0 3 +chrM 532 A 3 .., :II 0 0 0 0 3 +chrM 533 A 3 .., DGI 0 0 0 0 3 +chrM 534 A 3 .., III 0 0 0 0 3 +chrM 535 A 3 .., ?CI 0 0 0 0 3 +chrM 536 T 3 .., III 0 0 0 0 3 +chrM 537 A 3 .., 9II 0 0 0 0 3 +chrM 538 G 3 .., III 0 0 0 0 3 +chrM 539 C 3 .., III 0 0 0 0 3 +chrM 540 T 3 .., III 0 0 0 0 3 +chrM 541 T 3 .., III 0 0 0 0 3 +chrM 542 A 4 ..,^:. IIII 0 0 0 0 4 +chrM 543 C 4 ..,. IIII 0 0 0 0 4 +chrM 544 C 4 ..,. IIII 0 0 0 0 4 +chrM 545 A 4 N$.,. "III 0 0 0 0 3 +chrM 546 C 3 .,. III 0 0 0 0 3 +chrM 547 A 3 .,. DII 0 0 0 0 3 +chrM 548 A 3 .,. EII 0 0 0 0 3 +chrM 549 C 3 .,. III 0 0 0 0 3 +chrM 550 A 3 .,. III 0 0 0 0 3 +chrM 551 A 3 .,. 6II 0 0 0 0 3 +chrM 552 A 3 .,. GII 0 0 0 0 3 +chrM 553 G 3 .$,. ?II 0 0 0 0 3 +chrM 577 A 3 .$.^:. III 0 0 0 0 3 +chrM 580 A 3 ..^:, III 0 0 0 0 3 +chrM 581 G 3 .., III 0 0 0 0 3 +chrM 582 C 3 .., II? 0 0 0 0 3 +chrM 583 C 3 ..a II- 0 0 0 0 2 +chrM 584 T 3 .., IIH 0 0 0 0 3 +chrM 585 A 3 .., III 0 0 0 0 3 +chrM 586 A 3 .., III 0 0 0 0 3 +chrM 587 A 4 ..,^:, IIII 0 0 0 0 4 +chrM 588 A 4 ..,, IIII 0 0 0 0 4 +chrM 589 C 4 ..,, IIII 0 0 0 0 4 +chrM 590 T 4 ..,, II.5 0 0 0 0 3 +chrM 591 C 4 .$.,, II<I 0 0 0 0 4 +chrM 592 A 3 .,, III 0 0 0 0 3 +chrM 593 A 3 .,, III 0 0 0 0 3 +chrM 594 A 3 .,, III 0 0 0 0 3 +chrM 595 G 3 .,, III 0 0 0 0 3 +chrM 596 G 3 .,, III 0 0 0 0 3 +chrM 597 A 3 .,, :EI 0 0 0 0 3 +chrM 598 C 3 .,, III 0 0 0 0 3 +chrM 599 T 4 .,,^:. II@I 0 0 0 0 4 +chrM 600 T 4 .,,. IIII 0 0 0 0 4 +chrM 601 G 4 .,,. IIII 0 0 0 0 4 +chrM 602 G 4 .,,. IIII 0 0 0 0 4 +chrM 603 C 4 .,,. IIII 0 0 0 0 4 +chrM 604 G 4 .,,. IIII 0 0 0 0 4 +chrM 605 G 4 .,,. IIII 0 0 0 0 4 +chrM 606 T 4 .,,. 5III 0 0 0 0 4 +chrM 607 G 4 .,,. IIII 0 0 0 0 4 +chrM 608 C 4 .,,. *III 0 0 0 0 3 +chrM 609 T 5 .,,.^:, ?IIII 0 0 0 0 5 +chrM 610 T 5 .,,., IIII8 0 0 0 0 5 +chrM 611 T 5 .,,., IIIII 0 0 0 0 5 +chrM 612 A 5 T$,,., 3IIII 0 0 0 0 4 +chrM 613 C 4 ,,., III) 0 0 0 0 3 +chrM 614 A 4 ,,., IIII 0 0 0 0 4 +chrM 615 T 4 ,$,., IIII 0 0 0 0 4 +chrM 616 C 3 ,., III 0 0 0 0 3 +chrM 617 C 3 ,., III 0 0 0 0 3 +chrM 618 C 3 ,., III 0 0 0 0 3 +chrM 619 T 3 ,., IF9 0 0 0 0 3 +chrM 620 C 3 ,., II7 0 0 0 0 3 +chrM 621 T 3 ,., III 0 0 0 0 3 +chrM 622 A 3 ,$., I7I 0 0 0 0 3 +chrM 652 C 3 .,^:, II) 0 0 0 0 2 +chrM 653 G 3 .,, II2 0 0 0 0 2 +chrM 654 A 3 .,, III 0 0 0 0 3 +chrM 655 T 4 .,,^:. II*I 0 0 0 0 3 +chrM 656 A 4 .,,. IIII 0 0 0 0 4 +chrM 657 A 4 .,,. IIII 0 0 0 0 4 +chrM 658 A 4 .,,. IIII 0 0 0 0 4 +chrM 659 C 4 .,,. IIII 0 0 0 0 4 +chrM 660 C 4 .,,. IIII 0 0 0 0 4 +chrM 661 C 4 .,,. IIII 0 0 0 0 4 +chrM 662 C 4 .,,. IIFI 0 0 0 0 4 +chrM 663 A 4 .,,. =IDI 0 0 0 0 4 +chrM 664 C 4 .,,. II6I 0 0 0 0 4 +chrM 665 C 5 .,,.^:, IIIII 0 0 0 0 5 +chrM 666 A 5 .,,., BIIII 0 0 0 0 5 +chrM 667 T 5 .,,., II5I+ 0 0 0 0 4 +chrM 668 C 5 .,,., IIIII 0 0 0 0 5 +chrM 669 C 5 .,,., IIIII 0 0 0 0 5 +chrM 670 C 5 .,a., II.II 0 0 0 0 4 +chrM 671 T 5 .,,., IIIIA 0 0 0 0 5 +chrM 672 T 6 .,,.,^:. FI9I.I 0 0 0 0 5 +chrM 673 G 6 .,,.,. IIIIII 0 0 0 0 6 +chrM 674 C 6 .,,.,. IIIIII 0 0 0 0 6 +chrM 675 T 6 .,,.,. IIIIII 0 0 0 0 6 +chrM 676 A 6 .,,.,. ,IIEII 0 0 0 0 5 +chrM 677 A 7 .,,.,.^:. 3II;III 0 0 0 0 6 +chrM 678 T 7 .,,.,.. IIIIDII 0 0 0 0 7 +chrM 679 T 7 .,,.,.. CIIIIII 0 0 0 0 7 +chrM 680 C 7 .,,.,.. IIIIIII 0 0 0 0 7 +chrM 681 A 7 .$,,.,.. 9IIIIII 0 0 0 0 7 +chrM 682 G 6 ,,.,.. II$III 0 0 0 0 5 +chrM 683 C 6 ,,.,.. IIIIII 0 0 0 0 6 +chrM 684 C 6 ,$,.,.. IIIIII 0 0 0 0 6 +chrM 685 T 5 ,.,.. IIIII 0 0 0 0 5 +chrM 686 A 5 ,.,.. IIIII 0 0 0 0 5 +chrM 687 T 5 ,$.,.. IIIII 0 0 0 0 5 +chrM 688 A 4 .,.. IIII 0 0 0 0 4 +chrM 689 T 4 .,.. IIII 0 0 0 0 4 +chrM 690 A 4 .$,.. IIII 0 0 0 0 4 +chrM 691 C 3 ,.. III 0 0 0 0 3 +chrM 692 C 3 ,.. III 0 0 0 0 3 +chrM 693 G 4 ,..^:, IIII 0 0 0 0 4 +chrM 694 C 4 ,.., IIII 0 0 0 0 4 +chrM 695 C 4 ,.., IIII 0 0 0 0 4 +chrM 696 A 4 ,.., IIII 0 0 0 0 4 +chrM 697 T 4 ,.., IIII 0 0 0 0 4 +chrM 698 C 4 ,.., IIII 0 0 0 0 4 +chrM 699 T 4 ,.., IIII 0 0 0 0 4 +chrM 700 T 4 ,$.., IIII 0 0 0 0 4 +chrM 701 C 3 .., III 0 0 0 0 3 +chrM 702 A 3 .., III 0 0 0 0 3 +chrM 703 G 3 .., 2II 0 0 0 0 2 +chrM 704 C 3 .., III 0 0 0 0 3 +chrM 705 A 3 N., "II 0 0 0 0 2 +chrM 706 A 3 .., I5I 0 0 0 0 3 +chrM 707 A 3 .$., GII 0 0 0 0 3 +chrM 726 A 3 ,,^:. III 0 0 0 0 3 +chrM 727 G 3 ,,. III 0 0 0 0 3 +chrM 728 T 3 ,$,. III 0 0 0 0 3 +chrM 732 C 3 a.^:. $II 0 0 0 0 2 +chrM 733 A 3 ,.. III 0 0 0 0 3 +chrM 734 C 3 ,.. %II 0 0 0 0 2 +chrM 735 A 3 ,.. III 0 0 0 0 3 +chrM 736 A 3 ,.. *II 0 0 0 0 2 +chrM 737 A 3 ,.. III 0 0 0 0 3 +chrM 738 T 3 ,.. III 0 0 0 0 3 +chrM 739 A 3 ,.. III 0 0 0 0 3 +chrM 740 T 3 ,.. III 0 0 0 0 3 +chrM 741 C 3 ,.. III 0 0 0 0 3 +chrM 742 C 3 ,.. III 0 0 0 0 3 +chrM 743 A 3 ,.. III 0 0 0 0 3 +chrM 744 A 3 ,.. III 0 0 0 0 3 +chrM 745 C 3 ,.. III 0 0 0 0 3 +chrM 746 A 3 ,.. IIE 0 0 0 0 3 +chrM 747 T 3 ,.. III 0 0 0 0 3 +chrM 748 A 3 ,.. III 0 0 0 0 3 +chrM 749 A 3 ,.. III 0 0 0 0 3 +chrM 750 A 3 ,.. III 0 0 0 0 3 +chrM 751 A 3 ,.. IAI 0 0 0 0 3 +chrM 752 A 3 ,.. III 0 0 0 0 3 +chrM 753 C 3 ,.. III 0 0 0 0 3 +chrM 754 G 3 ,$.. III 0 0 0 0 3 +chrM 756 T 3 ..^:, III 0 0 0 0 3 +chrM 757 A 3 .., III 0 0 0 0 3 +chrM 758 G 3 .., III 0 0 0 0 3 +chrM 759 G 3 .., III 0 0 0 0 3 +chrM 760 T 3 .., =II 0 0 0 0 3 +chrM 761 C 3 .$., IID 0 0 0 0 3 +chrM 767 G 3 .$,^:, III 0 0 0 0 3 +chrM 769 A 3 ,,^:, III 0 0 0 0 3 +chrM 770 G 3 ,,, III 0 0 0 0 3 +chrM 771 C 3 ,,, IHI 0 0 0 0 3 +chrM 772 C 3 ,a, I)/ 0 0 0 0 1 +chrM 773 C 3 ,,, I7I 0 0 0 0 3 +chrM 774 A 4 ,,,^:. II:I 0 0 0 0 4 +chrM 775 T 4 ,,,. IH.I 0 0 0 0 3 +chrM 776 G 4 ,,,. IIII 0 0 0 0 4 +chrM 777 G 4 ,,,. IIII 0 0 0 0 4 +chrM 778 G 4 ,,,. IIII 0 0 0 0 4 +chrM 779 A 4 ,,,. IIAI 0 0 0 0 4 +chrM 780 T 4 ,,,. IIGI 0 0 0 0 4 +chrM 781 G 4 ,,,. IIII 0 0 0 0 4 +chrM 782 G 4 ,,,. IIII 0 0 0 0 4 +chrM 783 A 4 ,,,. IIII 0 0 0 0 4 +chrM 784 G 4 ,,,. IIII 0 0 0 0 4 +chrM 785 A 4 ,,,. IIII 0 0 0 0 4 +chrM 786 G 4 ,,,. IIII 0 0 0 0 4 +chrM 787 A 4 ,,,. IIII 0 0 0 0 4 +chrM 788 A 4 ,,,. IIII 0 0 0 0 4 +chrM 789 A 4 ,,,. IIII 0 0 0 0 4 +chrM 790 T 5 ,,,.^:. IIIII 0 0 0 0 5 +chrM 791 G 5 ,$,,.. IIIII 0 0 0 0 5 +chrM 792 G 4 ,,.. IIII 0 0 0 0 4 +chrM 793 G 4 ,,.. IIII 0 0 0 0 4 +chrM 794 C 4 ,,.. IIII 0 0 0 0 4 +chrM 795 T 4 ,,.. IIII 0 0 0 0 4 +chrM 796 A 4 ,,.. IIII 0 0 0 0 4 +chrM 797 C 4 ,,.. IIII 0 0 0 0 4 +chrM 798 A 4 ,,.. IIII 0 0 0 0 4 +chrM 799 T 4 ,,.. IIII 0 0 0 0 4 +chrM 800 T 4 ,,.. IIII 0 0 0 0 4 +chrM 801 T 4 ,,.. IIII 0 0 0 0 4 +chrM 802 T 4 ,$,.. IIII 0 0 0 0 4 +chrM 803 C 3 ,.. III 0 0 0 0 3 +chrM 804 T 3 ,$.. III 0 0 0 0 3 +chrM 806 C 3 ..^:. III 0 0 0 0 3 +chrM 807 C 3 ... III 0 0 0 0 3 +chrM 808 C 3 ... III 0 0 0 0 3 +chrM 809 T 3 .$.. III 0 0 0 0 3 +chrM 810 A 3 ..^:, III 0 0 0 0 3 +chrM 811 A 3 .., III 0 0 0 0 3 +chrM 812 G 3 .., II7 0 0 0 0 3 +chrM 813 A 3 .., III 0 0 0 0 3 +chrM 814 A 3 .., III 0 0 0 0 3 +chrM 815 C 3 .., III 0 0 0 0 3 +chrM 816 A 3 .., III 0 0 0 0 3 +chrM 817 A 3 .., III 0 0 0 0 3 +chrM 818 G 3 .., III 0 0 0 0 3 +chrM 819 A 3 .., III 0 0 0 0 3 +chrM 820 A 3 .., &II 0 0 0 0 2 +chrM 821 C 3 .., III 0 0 0 0 3 +chrM 822 T 3 .., III 0 0 0 0 3 +chrM 823 T 3 ..n II" 0 0 0 0 2 +chrM 824 T 3 .., III 0 0 0 0 3 +chrM 825 A 3 .$., III 0 0 0 0 3 +chrM 826 A 3 .,^:. III 0 0 0 0 3 +chrM 827 C 3 .,. III 0 0 0 0 3 +chrM 828 C 3 .,. III 0 0 0 0 3 +chrM 829 C 4 .,.^:, IIII 0 0 0 0 4 +chrM 830 G 4 .,., IIII 0 0 0 0 4 +chrM 831 G 4 .,., IIII 0 0 0 0 4 +chrM 832 A 4 .,., IIII 0 0 0 0 4 +chrM 833 C 4 .,., IIII 0 0 0 0 4 +chrM 834 G 4 .,., IIII 0 0 0 0 4 +chrM 835 A 4 .,., IIII 0 0 0 0 4 +chrM 836 A 4 .,., 8III 0 0 0 0 4 +chrM 837 A 4 .,., IIII 0 0 0 0 4 +chrM 838 G 4 .,., IIII 0 0 0 0 4 +chrM 839 T 5 .,.,^:, 4:IIG 0 0 0 0 4 +chrM 840 C 5 .,.,, IIIII 0 0 0 0 5 +chrM 841 T 5 .$,.,, IIIII 0 0 0 0 5 +chrM 842 C 4 ,.,, IIII 0 0 0 0 4 +chrM 843 C 4 ,.,, IIII 0 0 0 0 4 +chrM 844 A 4 ,.,, IIII 0 0 0 0 4 +chrM 845 T 4 ,$.,, IIII 0 0 0 0 4 +chrM 846 G 3 .,, @II 0 0 0 0 3 +chrM 847 A 3 .,, III 0 0 0 0 3 +chrM 848 A 3 .,, III 0 0 0 0 3 +chrM 849 A 3 .,, III 0 0 0 0 3 +chrM 850 C 3 .,, III 0 0 0 0 3 +chrM 851 T 3 .,, III 0 0 0 0 3 +chrM 852 G 3 .,, III 0 0 0 0 3 +chrM 853 G 3 .,, III 0 0 0 0 3 +chrM 854 A 3 .,, EII 0 0 0 0 3 +chrM 855 G 3 .,, DII 0 0 0 0 3 +chrM 856 A 3 .,, III 0 0 0 0 3 +chrM 857 C 3 .,, III 0 0 0 0 3 +chrM 858 T 4 .,,^:, IIIA 0 0 0 0 4 +chrM 859 A 4 .,,, @III 0 0 0 0 4 +chrM 860 A 4 .,,, IIII 0 0 0 0 4 +chrM 861 A 4 .$,,, EIII 0 0 0 0 4 +chrM 862 G 3 ,,, III 0 0 0 0 3 +chrM 863 G 3 ,,, III 0 0 0 0 3 +chrM 864 A 3 ,$,, III 0 0 0 0 3 +chrM 905 C 3 ,.^:, III 0 0 0 0 3 +chrM 906 A 3 ,., III 0 0 0 0 3 +chrM 907 G 3 ,., III 0 0 0 0 3 +chrM 908 G 3 ,., III 0 0 0 0 3 +chrM 909 C 3 ,., III 0 0 0 0 3 +chrM 910 C 3 ,., III 0 0 0 0 3 +chrM 911 A 4 ,.,^:, IIII 0 0 0 0 4 +chrM 912 T 4 ,.,, IIEG 0 0 0 0 4 +chrM 913 G 4 ,.,, III: 0 0 0 0 4 +chrM 914 A 4 ,.,, IIII 0 0 0 0 4 +chrM 915 A 4 ,.,, IIII 0 0 0 0 4 +chrM 916 G 4 ,.,, III5 0 0 0 0 4 +chrM 917 C 4 ,.,, III5 0 0 0 0 4 +chrM 918 G 4 ,.,, IIII 0 0 0 0 4 +chrM 919 C 4 ,.,, III< 0 0 0 0 4 +chrM 920 G 4 ,.,, IIII 0 0 0 0 4 +chrM 921 C 4 ,.,, IIII 0 0 0 0 4 +chrM 922 A 4 ,.,, IIII 0 0 0 0 4 +chrM 923 C 4 ,.,, III8 0 0 0 0 4 +chrM 924 A 4 ,.,, IFII 0 0 0 0 4 +chrM 925 C 4 ,.,, IIII 0 0 0 0 4 +chrM 926 A 4 ,.,, IIII 0 0 0 0 4 +chrM 927 C 4 ,.,, IIII 0 0 0 0 4 +chrM 928 C 5 ,.,,^:, IIII: 0 0 0 0 5 +chrM 929 G 5 ,.,,, IIIE: 0 0 0 0 5 +chrM 930 C 5 ,.,,, IIIII 0 0 0 0 5 +chrM 931 C 5 ,.,,, IIIIF 0 0 0 0 5 +chrM 932 C 5 ,.,,, IIIIC 0 0 0 0 5 +chrM 933 G 5 ,$.,,, I?II: 0 0 0 0 5 +chrM 934 T 4 .$,,, 4II> 0 0 0 0 3 +chrM 935 C 3 ,,, III 0 0 0 0 3 +chrM 936 A 3 ,,, III 0 0 0 0 3 +chrM 937 C 3 ,,, II1 0 0 0 0 2 +chrM 938 C 3 ,,, III 0 0 0 0 3 +chrM 939 C 3 ,,, III 0 0 0 0 3 +chrM 940 T 3 ,$,, III 0 0 0 0 3 +chrM 958 C 3 ,.^:. III 0 0 0 0 3 +chrM 959 A 3 ,.. III 0 0 0 0 3 +chrM 960 T 3 ,.. III 0 0 0 0 3 +chrM 961 A 3 ,.. III 0 0 0 0 3 +chrM 962 A 3 ,.. III 0 0 0 0 3 +chrM 963 C 4 ,$..^:. IIII 0 0 0 0 4 +chrM 964 A 3 ... I(; 0 0 0 0 2 +chrM 965 T 3 ... III 0 0 0 0 3 +chrM 966 A 4 ...^:. IIII 0 0 0 0 4 +chrM 967 A 4 .... IIII 0 0 0 0 4 +chrM 968 C 4 .... IEII 0 0 0 0 4 +chrM 969 A 4 .... IIII 0 0 0 0 4 +chrM 970 T 4 .... IIII 0 0 0 0 4 +chrM 971 A 4 .... IIII 0 0 0 0 4 +chrM 972 A 4 .... IIII 0 0 0 0 4 +chrM 973 A 4 .... II0I 0 0 0 0 3 +chrM 974 A 5 ....^:. IIIII 0 0 0 0 5 +chrM 975 C 5 ..... IIIII 0 0 0 0 5 +chrM 976 C 5 ..... IIIII 0 0 0 0 5 +chrM 977 G 5 ..... IIIII 0 0 0 0 5 +chrM 978 T 5 ..... IIIII 0 0 0 0 5 +chrM 979 G 5 ..... I0III 0 0 0 0 4 +chrM 980 A 5 ..... IIII4 0 0 0 0 4 +chrM 981 C 5 ..... IIIII 0 0 0 0 5 +chrM 982 C 5 ..... IIIII 0 0 0 0 5 +chrM 983 C 5 ..... IIIII 0 0 0 0 5 +chrM 984 A 5 ..... -IGII 0 0 0 0 4 +chrM 985 A 5 ..... 4GIII 0 0 0 0 4 +chrM 986 A 5 ..... BDGII 0 0 0 0 5 +chrM 987 C 5 ..... IDIII 0 0 0 0 5 +chrM 988 A 5 ..... @<III 0 0 0 0 5 +chrM 989 T 5 ..... IIIII 0 0 0 0 5 +chrM 990 A 5 .$.... I@III 0 0 0 0 5 +chrM 991 T 4 .... IICI 0 0 0 0 4 +chrM 992 G 4 T... )III 0 0 0 0 3 +chrM 993 A 4 .$... ?ICI 0 0 0 0 4 +chrM 994 A 3 ... III 0 0 0 0 3 +chrM 995 A 3 ... III 0 0 0 0 3 +chrM 996 G 3 ... III 0 0 0 0 3 +chrM 997 G 3 ... III 0 0 0 0 3 +chrM 998 A 3 .$.. 4II 0 0 0 0 2 +chrM 999 G 3 ..^:. III 0 0 0 0 3 +chrM 1000 A 3 ... III 0 0 0 0 3 +chrM 1001 C 3 .$.. III 0 0 0 0 3 +chrM 1043 A 3 ..^:, III 0 0 0 0 3 +chrM 1044 A 3 .., III 0 0 0 0 3 +chrM 1045 C 3 .., II7 0 0 0 0 3 +chrM 1046 C 3 .., II- 0 0 0 0 2 +chrM 1047 A 3 .., III 0 0 0 0 3 +chrM 1048 A 3 .., III 0 0 0 0 3 +chrM 1049 A 3 .., III 0 0 0 0 3 +chrM 1050 G 3 .., III 0 0 0 0 3 +chrM 1051 T 3 .., III 0 0 0 0 3 +chrM 1052 G 3 .., III 0 0 0 0 3 +chrM 1053 T 3 .., GII 0 0 0 0 3 +chrM 1054 A 3 .., III 0 0 0 0 3 +chrM 1055 G 3 .., :II 0 0 0 0 3 +chrM 1056 C 3 ..a HI% 0 0 0 0 2 +chrM 1057 T 3 .., III 0 0 0 0 3 +chrM 1058 T 3 .., III 0 0 0 0 3 +chrM 1059 A 3 .., BII 0 0 0 0 3 +chrM 1060 A 3 .., GII 0 0 0 0 3 +chrM 1061 A 3 .., HII 0 0 0 0 3 +chrM 1062 C 3 .., III 0 0 0 0 3 +chrM 1063 A 3 .., DII 0 0 0 0 3 +chrM 1064 A 3 .., BII 0 0 0 0 3 +chrM 1065 A 3 .., 1II 0 0 0 0 2 +chrM 1066 G 3 .$., &II 0 0 0 0 2 diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.6col.20-3-yes-no.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,2 @@ +chrM 270 C 4 a... ;III 1 0 0 0 4 +chrM 415 C 4 TTTt III7 0 0 0 4 4 diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.6col.20-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,2 @@ +chrM 269 270 C 4 a... ;III 1 0 0 0 4 +chrM 414 415 C 4 TTTt III7 0 0 0 4 4 diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.6col.40-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.40-3-yes-yes.pileup.out Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,1 @@ +chrM 414 415 C 4 TTTt III7 0 0 0 3 3 diff -r ba2412c2a4d9 -r adff03258b45 test-data/pileup_parser.6col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.pileup Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,1000 @@ +chrM 42 C 1 ^:. I +chrM 43 C 2 .^:. II +chrM 44 T 2 .. II +chrM 45 A 3 ..^:. III +chrM 46 G 4 ...^:. IIII +chrM 47 A 5 ....^:, IIIII +chrM 48 T 5 ...., IIIII +chrM 49 G 5 ...., IIIII +chrM 50 A 5 ...., IIIII +chrM 51 G 5 ...., IIIII +chrM 52 T 5 ...., IIIII +chrM 53 A 5 ...., IIIII +chrM 54 T 5 ...., IIIII +chrM 55 T 5 ...., IIIII +chrM 56 C 5 ...., IIIII +chrM 57 T 5 ...., IIIII +chrM 58 T 5 ...., IIIII +chrM 59 A 5 ...., IIIII +chrM 60 C 5 ...., IIIII +chrM 61 T 5 ...., IIIII +chrM 62 C 5 ...., IIIII +chrM 63 C 5 ...., IIIII +chrM 64 A 5 ...., IIIII +chrM 65 T 5 ...., IIIII +chrM 66 A 5 ...., IIIII +chrM 67 A 5 ...., IIIII +chrM 68 A 5 ...., IIICI +chrM 69 C 5 ...., IIIII +chrM 70 A 5 ...., IIIII +chrM 71 C 5 ...., IIIII +chrM 72 A 5 ...., IAIII +chrM 73 T 5 ...., IIIII +chrM 74 A 5 ...., IIIII +chrM 75 G 5 ...., %IIII +chrM 76 G 5 T..., *IIII +chrM 77 C 5 .$..., GIIII +chrM 78 T 4 .$.., IIII +chrM 79 T 3 .., III +chrM 80 G 3 .$., I1I +chrM 81 G 2 .$, II +chrM 82 T 1 ,$ I +chrM 83 C 2 ^:.^:. II +chrM 84 C 2 .. II +chrM 85 T 2 .. II +chrM 86 A 2 .. II +chrM 87 G 2 .. II +chrM 88 C 2 .. II +chrM 89 C 2 .. II +chrM 90 T 2 .. II +chrM 91 T 2 .. II +chrM 92 T 2 .. II +chrM 93 T 2 .. II +chrM 94 T 2 .. II +chrM 95 A 2 .. II +chrM 96 T 2 .. II +chrM 97 T 2 .. II +chrM 98 A 2 .. II +chrM 99 G 2 .. II +chrM 100 T 2 .. II +chrM 101 T 2 .. II +chrM 102 A 2 .. II +chrM 103 T 2 .. II +chrM 104 T 2 .. II +chrM 105 A 2 .. IE +chrM 106 A 2 .. II +chrM 107 T 2 .. II +chrM 108 A 2 .. II +chrM 109 G 2 .. II +chrM 110 A 2 .. II +chrM 111 A 2 .. I2 +chrM 112 T 2 .. II +chrM 113 T 2 .. II +chrM 114 A 2 .. H7 +chrM 115 C 2 .. II +chrM 116 A 2 .. II +chrM 117 C 2 .. II +chrM 118 A 2 .$.$ F8 +chrM 156 T 1 ^:, & +chrM 157 C 1 , I +chrM 158 A 2 g^:g I> +chrM 159 C 2 ,, /F +chrM 160 G 2 ,, II +chrM 161 T 2 ,, I> +chrM 162 C 2 ,, .- +chrM 163 T 2 ,, I8 +chrM 164 C 2 ,, 4F +chrM 165 T 2 ,, II +chrM 166 A 2 ,, II +chrM 167 C 2 ,, ;6 +chrM 168 G 2 ,, II +chrM 169 A 2 ,, II +chrM 170 T 2 ,, II +chrM 171 T 2 ,, IB +chrM 172 A 2 ,, II +chrM 173 A 2 ,, II +chrM 174 A 2 ,, II +chrM 175 A 2 ,, II +chrM 176 G 2 ,, II +chrM 177 G 2 ,, II +chrM 178 A 2 ,, II +chrM 179 G 2 ,, II +chrM 180 C 2 ,, II +chrM 181 A 3 ,,^:, III +chrM 182 G 3 ,,, III +chrM 183 G 3 ,,, III +chrM 184 T 3 ,,, III +chrM 185 A 3 ,,, III +chrM 186 T 3 ,,, III +chrM 187 C 3 ,,, III +chrM 188 A 3 ,,, III +chrM 189 A 3 ,,, III +chrM 190 G 3 ,,, III +chrM 191 C 3 ,$,, III +chrM 192 A 2 ,, II +chrM 193 C 2 ,$, II +chrM 194 A 1 , I +chrM 195 C 1 , I +chrM 196 T 1 , F +chrM 197 A 1 , I +chrM 198 G 1 , I +chrM 199 A 1 , I +chrM 200 A 1 , I +chrM 201 A 2 ,^:. I- +chrM 202 G 2 ,. II +chrM 203 T 2 ,. II +chrM 204 A 2 ,. II +chrM 205 G 2 ,. I6 +chrM 206 C 2 ,. II +chrM 207 T 2 ,. I, +chrM 208 C 2 ,. II +chrM 209 A 2 ,. II +chrM 210 T 2 ,. II +chrM 211 A 2 ,. II +chrM 212 A 2 ,. IE +chrM 213 C 2 ,. IC +chrM 214 A 2 ,. I; +chrM 215 C 2 ,. II +chrM 216 C 2 ,$. II +chrM 217 T 1 . I +chrM 218 T 1 . I +chrM 219 G 1 T I +chrM 220 C 1 . I +chrM 221 T 1 . I +chrM 222 C 1 . E +chrM 223 A 1 . 4 +chrM 224 G 1 T 9 +chrM 225 C 1 . : +chrM 226 C 1 . ? +chrM 227 A 1 . . +chrM 228 C 1 . C +chrM 229 A 3 .^:,^:, %II +chrM 230 C 3 .,, 8II +chrM 231 C 3 .,, 9II +chrM 232 C 3 .,, III +chrM 233 C 3 .,, AI' +chrM 234 C 3 .,, DI+ +chrM 235 A 3 .,, &I@ +chrM 236 C 3 .$,a +I$ +chrM 237 G 2 ,, II +chrM 238 G 2 ,, II +chrM 239 G 2 ,, II +chrM 240 A 2 ,, II +chrM 241 C 2 ,, I+ +chrM 242 A 2 ,, II +chrM 243 C 2 ,, II +chrM 244 A 3 ,,^:, II; +chrM 245 G 3 ,,, II* +chrM 246 C 3 ,,n II" +chrM 247 A 3 ,,, III +chrM 248 G 4 ,,,^:. IIII +chrM 249 T 4 ,,,. II)I +chrM 250 G 4 ,,,. II2I +chrM 251 A 4 ,,,. II(I +chrM 252 T 4 ,,,. II*I +chrM 253 A 4 ,,,. II7I +chrM 254 A 4 ,,,. II1I +chrM 255 A 4 ,,,. II?I +chrM 256 A 4 ,,,. II9I +chrM 257 A 4 ,,,. II?I +chrM 258 T 4 ,,,. II$I +chrM 259 T 5 ,,,.^:. II&II +chrM 260 A 5 ,,,.. II,II +chrM 261 A 5 ,,,.. II/II +chrM 262 G 5 ,,,.. II5II +chrM 263 C 5 ,,a.. II%II +chrM 264 T 5 ,$,$,.. II%II +chrM 265 A 3 ,.. )II +chrM 266 T 3 ,.. +II +chrM 267 G 4 ,..^:. *III +chrM 268 A 4 ,... EIII +chrM 269 A 4 ,... =III +chrM 270 C 4 a... ;III +chrM 271 G 4 ,... ;III +chrM 272 A 4 ,... 8@II +chrM 273 A 4 ,... 1III +chrM 274 A 4 ,... ICII +chrM 275 G 4 ,... IIII +chrM 276 T 4 ,... IIII +chrM 277 T 4 ,... IIII +chrM 278 C 4 ,... IIII +chrM 279 G 4 ,$... IIII +chrM 280 A 3 ... III +chrM 281 C 3 ... GII +chrM 282 T 3 ... III +chrM 283 A 3 .$.. IFI +chrM 284 A 3 ..^:, IAI +chrM 285 G 3 .., ;II +chrM 286 T 4 ..,^:. IIII +chrM 287 C 4 ..,. II4I +chrM 288 A 4 ..,. @III +chrM 289 T 4 ..,. IIII +chrM 290 A 4 ..,. @:II +chrM 291 T 4 ..,. IIAI +chrM 292 T 4 ..,. IIII +chrM 293 A 4 ..,. 8;II +chrM 294 A 4 .$.,. I<II +chrM 295 A 3 .,. 4II +chrM 296 T 3 .,. III +chrM 297 A 3 .,. BII +chrM 298 A 3 .,. CII +chrM 299 G 3 .,. III +chrM 300 G 3 .,. ;II +chrM 301 G 3 .,. III +chrM 302 T 3 .$,. III +chrM 303 T 2 ,. II +chrM 304 G 2 ,. II +chrM 305 G 2 ,. II +chrM 306 T 2 ,. II +chrM 307 A 2 ,. II +chrM 308 A 2 ,. II +chrM 309 A 2 ,. II +chrM 310 T 2 ,. II +chrM 311 T 2 ,. II +chrM 312 T 3 ,.^:. III +chrM 313 C 3 ,.. III +chrM 314 G 3 ,.. III +chrM 315 T 3 ,.. III +chrM 316 G 3 ,.. III +chrM 317 C 3 ,.. III +chrM 318 C 3 ,.. III +chrM 319 A 3 ,$.. III +chrM 320 G 2 .. II +chrM 321 C 2 .$. II +chrM 322 C 1 . I +chrM 323 A 1 . I +chrM 324 C 1 . I +chrM 325 C 1 . I +chrM 326 G 1 . I +chrM 327 C 1 . I +chrM 328 G 1 . I +chrM 329 G 1 . I +chrM 330 T 1 . I +chrM 331 C 1 . I +chrM 332 A 1 . I +chrM 333 T 1 . I +chrM 334 A 1 . I +chrM 335 C 1 . I +chrM 336 G 1 . I +chrM 337 A 1 . I +chrM 338 T 1 . I +chrM 339 T 1 . I +chrM 340 A 1 . I +chrM 341 A 1 . D +chrM 342 C 1 . I +chrM 343 C 1 . I +chrM 344 C 1 . I +chrM 345 A 1 . I +chrM 346 A 1 . ; +chrM 347 A 1 .$ 7 +chrM 360 C 1 ^:. I +chrM 361 G 1 . I +chrM 362 G 1 . I +chrM 363 C 1 . I +chrM 364 G 1 . I +chrM 365 T 1 . I +chrM 366 A 1 . I +chrM 367 A 1 . I +chrM 368 A 1 . I +chrM 369 G 1 . I +chrM 370 C 1 . I +chrM 371 G 1 . I +chrM 372 T 1 . I +chrM 373 G 1 . I +chrM 374 T 1 . I +chrM 375 C 1 . I +chrM 376 A 1 . I +chrM 377 A 1 . I +chrM 378 A 1 . I +chrM 379 G 1 . I +chrM 380 A 1 . I +chrM 381 C 1 T I +chrM 382 T 1 . I +chrM 383 A 1 . I +chrM 384 A 1 . I +chrM 385 T 1 . I +chrM 386 A 1 G I +chrM 387 C 1 . I +chrM 388 C 1 . I +chrM 389 A 2 .^:. II +chrM 390 A 3 ..^:. III +chrM 391 A 3 ... >II +chrM 392 A 3 ... III +chrM 393 T 3 ... III +chrM 394 A 3 ... III +chrM 395 A 3 .$.. III +chrM 396 A 2 .. II +chrM 397 G 2 .. II +chrM 398 T 2 .. EI +chrM 399 T 2 .. II +chrM 400 A 3 ..^:. III +chrM 401 A 3 ... III +chrM 402 A 3 ... III +chrM 403 A 3 ... III +chrM 404 C 3 ... III +chrM 405 C 3 ... III +chrM 406 C 3 ... EII +chrM 407 A 3 ... III +chrM 408 G 3 ... III +chrM 409 T 3 ... 0II +chrM 410 T 3 ... III +chrM 411 A 4 ...^:, IIII +chrM 412 A 4 ..., FIII +chrM 413 G 4 ..., IIIH +chrM 414 C 4 ...a III2 +chrM 415 C 4 TTTt III7 +chrM 416 G 5 ...,^:, II?7: +chrM 417 T 5 ...,, ;IIE@ +chrM 418 A 5 ...,, IIIII +chrM 419 A 5 ...,, IIIII +chrM 420 A 5 ...,, FIIII +chrM 421 A 5 ...,, IIIII +chrM 422 A 5 ...,, >IIII +chrM 423 G 6 ...,,^:, HII/I, +chrM 424 C 6 .$..a,, ;II-I: +chrM 425 T 5 .$.,,, IIIIF +chrM 426 A 5 .,,,^:, III@I +chrM 427 C 5 .,,,, III$I +chrM 428 A 5 .,,,, IIIII +chrM 429 A 5 .,,,, IIII. +chrM 430 C 5 .,,,a I%I5' +chrM 431 C 5 .,,,, I(I5< +chrM 432 A 5 .,,,, IIIII +chrM 433 A 5 .,,,, 0IIII +chrM 434 A 5 .,,,, =IIII +chrM 435 G 5 .$,,,, EIIII +chrM 436 T 4 ,,,, III5 +chrM 437 A 4 ,,,, IIII +chrM 438 A 4 ,,,, IIII +chrM 439 A 4 ,,,, IIII +chrM 440 A 4 ,,,, IIIF +chrM 441 T 6 ,,,,^:.^:. III;II +chrM 442 A 6 ,,,,.. IIIIII +chrM 443 G 6 ,,,,.. IIIIII +chrM 444 A 6 ,,,,.. IIIIII +chrM 445 C 6 ,,,,.. IIIIII +chrM 446 T 6 ,$,,,.. IIIIII +chrM 447 A 5 ,,,.. IIIII +chrM 448 C 5 ,,,.. IIIII +chrM 449 G 6 ,,,..^:, IIIII6 +chrM 450 A 6 ,,,.., IIIIII +chrM 451 A 6 ,$,,.., IIIIII +chrM 452 A 5 ,,.., IIIII +chrM 453 G 5 ,,.., IIIII +chrM 454 T 6 ,,..,^:, IIIIII +chrM 455 G 6 ,,..,, IIIIII +chrM 456 A 6 ,,..,, IIIIII +chrM 457 C 6 ,,..,, IIIII= +chrM 458 T 6 ,$,..,, IIIIII +chrM 459 T 5 ,..,, IIIII +chrM 460 T 5 ,..,, IIIII +chrM 461 A 5 ,$..,, IIIII +chrM 462 A 4 ..,, IIII +chrM 463 T 4 ..,, IIIC +chrM 464 A 4 ..,, IIII +chrM 465 C 4 ..,, IIII +chrM 466 C 4 ..,, IIII +chrM 467 T 4 ..,, II>? +chrM 468 C 4 ..,, IIII +chrM 469 T 4 ..,, IIIG +chrM 470 G 4 ..,, %III +chrM 471 A 4 ..,, 4;II +chrM 472 C 4 ..,, II3I +chrM 473 T 4 ..,, IIII +chrM 474 A 4 ..,, ;III +chrM 475 C 4 ..,, IIII +chrM 476 A 4 .$.$,, 32II +chrM 477 C 2 ,, II +chrM 478 G 2 ,, II +chrM 479 A 2 ,, II +chrM 480 T 3 ,,^:. III +chrM 481 A 3 ,,. III +chrM 482 G 3 ,,. III +chrM 483 C 4 ,,.^:, IIIE +chrM 484 T 4 ,$,., III9 +chrM 485 A 3 ,., III +chrM 486 A 3 ,., III +chrM 487 G 3 ,., III +chrM 488 A 3 ,., III +chrM 489 C 3 ,$., III +chrM 490 C 2 ., II +chrM 491 C 2 ., II +chrM 492 A 2 ., II +chrM 493 A 2 ., II +chrM 494 A 2 ., II +chrM 495 C 2 ., II +chrM 496 T 2 ., I2 +chrM 497 G 2 ., II +chrM 498 G 2 ., II +chrM 499 G 2 ., II +chrM 500 A 2 ., II +chrM 501 T 2 ., II +chrM 502 T 2 ., II +chrM 503 A 2 ., II +chrM 504 G 2 ., II +chrM 505 A 2 ., GI +chrM 506 T 2 ., II +chrM 507 A 2 ., II +chrM 508 C 2 ., II +chrM 509 C 2 ., II +chrM 510 C 3 .,^:. III +chrM 511 C 3 .,. III +chrM 512 A 3 .,. 6II +chrM 513 C 3 .,. III +chrM 514 T 3 .,. III +chrM 515 A 3 .$,. III +chrM 516 T 2 ,. II +chrM 517 G 2 ,. II +chrM 518 C 3 ,$.^:. III +chrM 519 T 2 .. II +chrM 520 T 3 ..^:, III +chrM 521 A 3 .., III +chrM 522 G 3 .., II, +chrM 523 C 3 .., III +chrM 524 C 3 .., II7 +chrM 525 C 3 .., III +chrM 526 T 3 .., II? +chrM 527 A 3 .., III +chrM 528 A 3 .., III +chrM 529 A 3 .., FII +chrM 530 C 3 .., II+ +chrM 531 T 3 .., III +chrM 532 A 3 .., :II +chrM 533 A 3 .., DGI +chrM 534 A 3 .., III +chrM 535 A 3 .., ?CI +chrM 536 T 3 .., III +chrM 537 A 3 .., 9II +chrM 538 G 3 .., III +chrM 539 C 3 .., III +chrM 540 T 3 .., III +chrM 541 T 3 .., III +chrM 542 A 4 ..,^:. IIII +chrM 543 C 4 ..,. IIII +chrM 544 C 4 ..,. IIII +chrM 545 A 4 N$.,. "III +chrM 546 C 3 .,. III +chrM 547 A 3 .,. DII +chrM 548 A 3 .,. EII +chrM 549 C 3 .,. III +chrM 550 A 3 .,. III +chrM 551 A 3 .,. 6II +chrM 552 A 3 .,. GII +chrM 553 G 3 .$,. ?II +chrM 554 C 2 ,. I< +chrM 555 T 2 ,$. II +chrM 556 A 2 .^:. II +chrM 557 T 2 .. II +chrM 558 T 2 .. II +chrM 559 C 2 .. II +chrM 560 G 2 .. II +chrM 561 C 2 .. II +chrM 562 C 2 .. II +chrM 563 A 2 .. CI +chrM 564 G 2 .. II +chrM 565 A 2 .. GI +chrM 566 G 2 .. II +chrM 567 T 2 .. /I +chrM 568 A 2 .. DI +chrM 569 C 2 .. II +chrM 570 T 2 .. II +chrM 571 A 2 .. II +chrM 572 C 2 .. FI +chrM 573 T 2 .. 9I +chrM 574 A 2 .. II +chrM 575 G 2 .. II +chrM 576 C 2 .. II +chrM 577 A 3 .$.^:. III +chrM 578 A 2 .. II +chrM 579 C 2 .. II +chrM 580 A 3 ..^:, III +chrM 581 G 3 .., III +chrM 582 C 3 .., II? +chrM 583 C 3 ..a II- +chrM 584 T 3 .., IIH +chrM 585 A 3 .., III +chrM 586 A 3 .., III +chrM 587 A 4 ..,^:, IIII +chrM 588 A 4 ..,, IIII +chrM 589 C 4 ..,, IIII +chrM 590 T 4 ..,, II.5 +chrM 591 C 4 .$.,, II<I +chrM 592 A 3 .,, III +chrM 593 A 3 .,, III +chrM 594 A 3 .,, III +chrM 595 G 3 .,, III +chrM 596 G 3 .,, III +chrM 597 A 3 .,, :EI +chrM 598 C 3 .,, III +chrM 599 T 4 .,,^:. II@I +chrM 600 T 4 .,,. IIII +chrM 601 G 4 .,,. IIII +chrM 602 G 4 .,,. IIII +chrM 603 C 4 .,,. IIII +chrM 604 G 4 .,,. IIII +chrM 605 G 4 .,,. IIII +chrM 606 T 4 .,,. 5III +chrM 607 G 4 .,,. IIII +chrM 608 C 4 .,,. *III +chrM 609 T 5 .,,.^:, ?IIII +chrM 610 T 5 .,,., IIII8 +chrM 611 T 5 .,,., IIIII +chrM 612 A 5 T$,,., 3IIII +chrM 613 C 4 ,,., III) +chrM 614 A 4 ,,., IIII +chrM 615 T 4 ,$,., IIII +chrM 616 C 3 ,., III +chrM 617 C 3 ,., III +chrM 618 C 3 ,., III +chrM 619 T 3 ,., IF9 +chrM 620 C 3 ,., II7 +chrM 621 T 3 ,., III +chrM 622 A 3 ,$., I7I +chrM 623 G 2 ., II +chrM 624 A 2 ., 9I +chrM 625 G 2 ., II +chrM 626 G 2 ., II +chrM 627 A 2 ., 2I +chrM 628 G 2 ., II +chrM 629 C 2 ., II +chrM 630 C 2 ., II +chrM 631 T 2 ., II +chrM 632 G 2 ., II +chrM 633 T 2 ., II +chrM 634 T 2 .$, II +chrM 635 C 1 , I +chrM 636 C 1 , I +chrM 637 A 1 , I +chrM 638 T 1 , I +chrM 639 A 1 , I +chrM 640 A 1 , I +chrM 641 T 1 , I +chrM 642 C 1 , I +chrM 643 G 1 , I +chrM 644 A 1 ,$ I +chrM 646 A 1 ^:. I +chrM 647 A 1 . I +chrM 648 A 1 . I +chrM 649 C 2 .^:, II +chrM 650 C 2 ., II +chrM 651 C 2 ., II +chrM 652 C 3 .,^:, II) +chrM 653 G 3 .,, II2 +chrM 654 A 3 .,, III +chrM 655 T 4 .,,^:. II*I +chrM 656 A 4 .,,. IIII +chrM 657 A 4 .,,. IIII +chrM 658 A 4 .,,. IIII +chrM 659 C 4 .,,. IIII +chrM 660 C 4 .,,. IIII +chrM 661 C 4 .,,. IIII +chrM 662 C 4 .,,. IIFI +chrM 663 A 4 .,,. =IDI +chrM 664 C 4 .,,. II6I +chrM 665 C 5 .,,.^:, IIIII +chrM 666 A 5 .,,., BIIII +chrM 667 T 5 .,,., II5I+ +chrM 668 C 5 .,,., IIIII +chrM 669 C 5 .,,., IIIII +chrM 670 C 5 .,a., II.II +chrM 671 T 5 .,,., IIIIA +chrM 672 T 6 .,,.,^:. FI9I.I +chrM 673 G 6 .,,.,. IIIIII +chrM 674 C 6 .,,.,. IIIIII +chrM 675 T 6 .,,.,. IIIIII +chrM 676 A 6 .,,.,. ,IIEII +chrM 677 A 7 .,,.,.^:. 3II;III +chrM 678 T 7 .,,.,.. IIIIDII +chrM 679 T 7 .,,.,.. CIIIIII +chrM 680 C 7 .,,.,.. IIIIIII +chrM 681 A 7 .$,,.,.. 9IIIIII +chrM 682 G 6 ,,.,.. II$III +chrM 683 C 6 ,,.,.. IIIIII +chrM 684 C 6 ,$,.,.. IIIIII +chrM 685 T 5 ,.,.. IIIII +chrM 686 A 5 ,.,.. IIIII +chrM 687 T 5 ,$.,.. IIIII +chrM 688 A 4 .,.. IIII +chrM 689 T 4 .,.. IIII +chrM 690 A 4 .$,.. IIII +chrM 691 C 3 ,.. III +chrM 692 C 3 ,.. III +chrM 693 G 4 ,..^:, IIII +chrM 694 C 4 ,.., IIII +chrM 695 C 4 ,.., IIII +chrM 696 A 4 ,.., IIII +chrM 697 T 4 ,.., IIII +chrM 698 C 4 ,.., IIII +chrM 699 T 4 ,.., IIII +chrM 700 T 4 ,$.., IIII +chrM 701 C 3 .., III +chrM 702 A 3 .., III +chrM 703 G 3 .., 2II +chrM 704 C 3 .., III +chrM 705 A 3 N., "II +chrM 706 A 3 .., I5I +chrM 707 A 3 .$., GII +chrM 708 C 2 ., II +chrM 709 C 2 ., II +chrM 710 C 2 ., II +chrM 711 T 2 ., II +chrM 712 A 2 .$, II +chrM 713 A 1 , I +chrM 714 A 1 , I +chrM 715 C 1 , I +chrM 716 A 1 , I +chrM 717 A 1 , I +chrM 718 G 1 , I +chrM 719 G 2 ,^:, I& +chrM 720 T 2 ,g I$ +chrM 721 A 2 ,, I3 +chrM 722 C 2 ,, I$ +chrM 723 C 2 ,t I& +chrM 724 G 2 ,, I) +chrM 725 A 2 ,, II +chrM 726 A 3 ,,^:. III +chrM 727 G 3 ,,. III +chrM 728 T 3 ,$,. III +chrM 729 A 2 ,. II +chrM 730 A 2 n. "I +chrM 731 G 2 ,. II +chrM 732 C 3 a.^:. $II +chrM 733 A 3 ,.. III +chrM 734 C 3 ,.. %II +chrM 735 A 3 ,.. III +chrM 736 A 3 ,.. *II +chrM 737 A 3 ,.. III +chrM 738 T 3 ,.. III +chrM 739 A 3 ,.. III +chrM 740 T 3 ,.. III +chrM 741 C 3 ,.. III +chrM 742 C 3 ,.. III +chrM 743 A 3 ,.. III +chrM 744 A 3 ,.. III +chrM 745 C 3 ,.. III +chrM 746 A 3 ,.. IIE +chrM 747 T 3 ,.. III +chrM 748 A 3 ,.. III +chrM 749 A 3 ,.. III +chrM 750 A 3 ,.. III +chrM 751 A 3 ,.. IAI +chrM 752 A 3 ,.. III +chrM 753 C 3 ,.. III +chrM 754 G 3 ,$.. III +chrM 755 T 2 .. II +chrM 756 T 3 ..^:, III +chrM 757 A 3 .., III +chrM 758 G 3 .., III +chrM 759 G 3 .., III +chrM 760 T 3 .., =II +chrM 761 C 3 .$., IID +chrM 762 A 2 ., =I +chrM 763 A 2 ., EI +chrM 764 G 2 ., II +chrM 765 G 2 ., II +chrM 766 T 2 ., :I +chrM 767 G 3 .$,^:, III +chrM 768 T 2 ,, I> +chrM 769 A 3 ,,^:, III +chrM 770 G 3 ,,, III +chrM 771 C 3 ,,, IHI +chrM 772 C 3 ,a, I)/ +chrM 773 C 3 ,,, I7I +chrM 774 A 4 ,,,^:. II:I +chrM 775 T 4 ,,,. IH.I +chrM 776 G 4 ,,,. IIII +chrM 777 G 4 ,,,. IIII +chrM 778 G 4 ,,,. IIII +chrM 779 A 4 ,,,. IIAI +chrM 780 T 4 ,,,. IIGI +chrM 781 G 4 ,,,. IIII +chrM 782 G 4 ,,,. IIII +chrM 783 A 4 ,,,. IIII +chrM 784 G 4 ,,,. IIII +chrM 785 A 4 ,,,. IIII +chrM 786 G 4 ,,,. IIII +chrM 787 A 4 ,,,. IIII +chrM 788 A 4 ,,,. IIII +chrM 789 A 4 ,,,. IIII +chrM 790 T 5 ,,,.^:. IIIII +chrM 791 G 5 ,$,,.. IIIII +chrM 792 G 4 ,,.. IIII +chrM 793 G 4 ,,.. IIII +chrM 794 C 4 ,,.. IIII +chrM 795 T 4 ,,.. IIII +chrM 796 A 4 ,,.. IIII +chrM 797 C 4 ,,.. IIII +chrM 798 A 4 ,,.. IIII +chrM 799 T 4 ,,.. IIII +chrM 800 T 4 ,,.. IIII +chrM 801 T 4 ,,.. IIII +chrM 802 T 4 ,$,.. IIII +chrM 803 C 3 ,.. III +chrM 804 T 3 ,$.. III +chrM 805 A 2 .. II +chrM 806 C 3 ..^:. III +chrM 807 C 3 ... III +chrM 808 C 3 ... III +chrM 809 T 3 .$.. III +chrM 810 A 3 ..^:, III +chrM 811 A 3 .., III +chrM 812 G 3 .., II7 +chrM 813 A 3 .., III +chrM 814 A 3 .., III +chrM 815 C 3 .., III +chrM 816 A 3 .., III +chrM 817 A 3 .., III +chrM 818 G 3 .., III +chrM 819 A 3 .., III +chrM 820 A 3 .., &II +chrM 821 C 3 .., III +chrM 822 T 3 .., III +chrM 823 T 3 ..n II" +chrM 824 T 3 .., III +chrM 825 A 3 .$., III +chrM 826 A 3 .,^:. III +chrM 827 C 3 .,. III +chrM 828 C 3 .,. III +chrM 829 C 4 .,.^:, IIII +chrM 830 G 4 .,., IIII +chrM 831 G 4 .,., IIII +chrM 832 A 4 .,., IIII +chrM 833 C 4 .,., IIII +chrM 834 G 4 .,., IIII +chrM 835 A 4 .,., IIII +chrM 836 A 4 .,., 8III +chrM 837 A 4 .,., IIII +chrM 838 G 4 .,., IIII +chrM 839 T 5 .,.,^:, 4:IIG +chrM 840 C 5 .,.,, IIIII +chrM 841 T 5 .$,.,, IIIII +chrM 842 C 4 ,.,, IIII +chrM 843 C 4 ,.,, IIII +chrM 844 A 4 ,.,, IIII +chrM 845 T 4 ,$.,, IIII +chrM 846 G 3 .,, @II +chrM 847 A 3 .,, III +chrM 848 A 3 .,, III +chrM 849 A 3 .,, III +chrM 850 C 3 .,, III +chrM 851 T 3 .,, III +chrM 852 G 3 .,, III +chrM 853 G 3 .,, III +chrM 854 A 3 .,, EII +chrM 855 G 3 .,, DII +chrM 856 A 3 .,, III +chrM 857 C 3 .,, III +chrM 858 T 4 .,,^:, IIIA +chrM 859 A 4 .,,, @III +chrM 860 A 4 .,,, IIII +chrM 861 A 4 .$,,, EIII +chrM 862 G 3 ,,, III +chrM 863 G 3 ,,, III +chrM 864 A 3 ,$,, III +chrM 865 G 2 ,, II +chrM 866 G 2 ,, II +chrM 867 A 2 ,, II +chrM 868 T 2 ,, II +chrM 869 T 2 ,, II +chrM 870 T 2 ,, II +chrM 871 A 2 ,, II +chrM 872 G 2 ,, II +chrM 873 C 2 ,, II +chrM 874 A 2 ,$, II +chrM 875 G 1 , I +chrM 876 T 1 , I +chrM 877 A 1 , I +chrM 878 A 1 , I +chrM 879 A 1 , I +chrM 880 T 1 , I +chrM 881 T 1 , I +chrM 882 A 1 , I +chrM 883 A 1 , I +chrM 884 G 1 , I +chrM 885 A 1 , I +chrM 886 A 1 , I +chrM 887 T 1 , ( +chrM 888 A 1 , I +chrM 889 G 1 , I +chrM 890 A 1 , I +chrM 891 G 1 , I +chrM 892 A 1 , I +chrM 893 G 1 ,$ I +chrM 898 A 1 ^:, I +chrM 899 T 2 ,^:. /I +chrM 900 T 2 ,. 7I +chrM 901 G 2 ,. CI +chrM 902 A 2 ,. II +chrM 903 A 2 ,. II +chrM 904 T 2 ,. II +chrM 905 C 3 ,.^:, III +chrM 906 A 3 ,., III +chrM 907 G 3 ,., III +chrM 908 G 3 ,., III +chrM 909 C 3 ,., III +chrM 910 C 3 ,., III +chrM 911 A 4 ,.,^:, IIII +chrM 912 T 4 ,.,, IIEG +chrM 913 G 4 ,.,, III: +chrM 914 A 4 ,.,, IIII +chrM 915 A 4 ,.,, IIII +chrM 916 G 4 ,.,, III5 +chrM 917 C 4 ,.,, III5 +chrM 918 G 4 ,.,, IIII +chrM 919 C 4 ,.,, III< +chrM 920 G 4 ,.,, IIII +chrM 921 C 4 ,.,, IIII +chrM 922 A 4 ,.,, IIII +chrM 923 C 4 ,.,, III8 +chrM 924 A 4 ,.,, IFII +chrM 925 C 4 ,.,, IIII +chrM 926 A 4 ,.,, IIII +chrM 927 C 4 ,.,, IIII +chrM 928 C 5 ,.,,^:, IIII: +chrM 929 G 5 ,.,,, IIIE: +chrM 930 C 5 ,.,,, IIIII +chrM 931 C 5 ,.,,, IIIIF +chrM 932 C 5 ,.,,, IIIIC +chrM 933 G 5 ,$.,,, I?II: +chrM 934 T 4 .$,,, 4II> +chrM 935 C 3 ,,, III +chrM 936 A 3 ,,, III +chrM 937 C 3 ,,, II1 +chrM 938 C 3 ,,, III +chrM 939 C 3 ,,, III +chrM 940 T 3 ,$,, III +chrM 941 C 2 ,, II +chrM 942 C 2 ,, I' +chrM 943 T 2 ,, II +chrM 944 T 2 ,, II +chrM 945 A 2 ,, II +chrM 946 A 2 ,$, II +chrM 947 A 1 , I +chrM 948 T 1 , I +chrM 949 A 1 , I +chrM 950 T 1 , I +chrM 951 C 1 , I +chrM 952 A 1 , I +chrM 953 C 1 , I +chrM 954 A 1 , I +chrM 955 A 2 ,^:. II +chrM 956 A 2 ,. II +chrM 957 T 2 ,. II +chrM 958 C 3 ,.^:. III +chrM 959 A 3 ,.. III +chrM 960 T 3 ,.. III +chrM 961 A 3 ,.. III +chrM 962 A 3 ,.. III +chrM 963 C 4 ,$..^:. IIII +chrM 964 A 3 ... I(; +chrM 965 T 3 ... III +chrM 966 A 4 ...^:. IIII +chrM 967 A 4 .... IIII +chrM 968 C 4 .... IEII +chrM 969 A 4 .... IIII +chrM 970 T 4 .... IIII +chrM 971 A 4 .... IIII +chrM 972 A 4 .... IIII +chrM 973 A 4 .... II0I +chrM 974 A 5 ....^:. IIIII +chrM 975 C 5 ..... IIIII +chrM 976 C 5 ..... IIIII +chrM 977 G 5 ..... IIIII +chrM 978 T 5 ..... IIIII +chrM 979 G 5 ..... I0III +chrM 980 A 5 ..... IIII4 +chrM 981 C 5 ..... IIIII +chrM 982 C 5 ..... IIIII +chrM 983 C 5 ..... IIIII +chrM 984 A 5 ..... -IGII +chrM 985 A 5 ..... 4GIII +chrM 986 A 5 ..... BDGII +chrM 987 C 5 ..... IDIII +chrM 988 A 5 ..... @<III +chrM 989 T 5 ..... IIIII +chrM 990 A 5 .$.... I@III +chrM 991 T 4 .... IICI +chrM 992 G 4 T... )III +chrM 993 A 4 .$... ?ICI +chrM 994 A 3 ... III +chrM 995 A 3 ... III +chrM 996 G 3 ... III +chrM 997 G 3 ... III +chrM 998 A 3 .$.. 4II +chrM 999 G 3 ..^:. III +chrM 1000 A 3 ... III +chrM 1001 C 3 .$.. III +chrM 1002 A 2 .. II +chrM 1003 A 2 .. II +chrM 1004 G 2 .. II +chrM 1005 T 2 .. II +chrM 1006 C 2 .. II +chrM 1007 G 2 .. CI +chrM 1008 T 2 .. II +chrM 1009 A 2 .$. II +chrM 1010 A 1 . I +chrM 1011 C 1 . I +chrM 1012 A 1 . I +chrM 1013 A 1 . I +chrM 1014 G 1 . I +chrM 1015 G 1 . I +chrM 1016 T 1 . I +chrM 1017 A 1 . I +chrM 1018 A 1 . I +chrM 1019 G 1 . I +chrM 1020 T 1 . I +chrM 1021 A 1 . I +chrM 1022 T 1 . I +chrM 1023 A 1 . I +chrM 1024 C 1 . I +chrM 1025 C 1 . I +chrM 1026 G 1 . I +chrM 1027 G 1 . I +chrM 1028 A 1 . I +chrM 1029 A 1 . I +chrM 1030 G 1 . I +chrM 1031 G 2 .^:. II +chrM 1032 T 2 .. EI +chrM 1033 G 2 .. II +chrM 1034 T 2 .$. II +chrM 1035 A 2 .^:. II +chrM 1036 C 2 .. II +chrM 1037 T 2 .. II +chrM 1038 T 2 .. II +chrM 1039 G 2 .. II +chrM 1040 G 2 .. II +chrM 1041 A 2 .. II +chrM 1042 T 2 .. II +chrM 1043 A 3 ..^:, III +chrM 1044 A 3 .., III +chrM 1045 C 3 .., II7 +chrM 1046 C 3 .., II- +chrM 1047 A 3 .., III +chrM 1048 A 3 .., III +chrM 1049 A 3 .., III +chrM 1050 G 3 .., III +chrM 1051 T 3 .., III +chrM 1052 G 3 .., III +chrM 1053 T 3 .., GII +chrM 1054 A 3 .., III +chrM 1055 G 3 .., :II +chrM 1056 C 3 ..a HI% +chrM 1057 T 3 .., III +chrM 1058 T 3 .., III +chrM 1059 A 3 .., BII +chrM 1060 A 3 .., GII +chrM 1061 A 3 .., HII +chrM 1062 C 3 .., III +chrM 1063 A 3 .., DII +chrM 1064 A 3 .., BII +chrM 1065 A 3 .., 1II +chrM 1066 G 3 .$., &II +chrM 1067 C 2 ., II +chrM 1068 A 2 ., II +chrM 1069 T 2 ., II +chrM 1070 C 2 .$, II +chrM 1071 C 1 , I +chrM 1072 A 1 , I +chrM 1073 G 1 , I +chrM 1074 C 1 , I +chrM 1075 T 1 , I +chrM 1076 T 1 , I +chrM 1077 A 1 , I +chrM 1078 C 1 ,$ I +chrM 1090 T 1 ^:, I +chrM 1091 T 1 , I +chrM 1092 C 1 n " +chrM 1093 A 1 , I +chrM 1094 C 1 , I +chrM 1095 T 1 , 7 +chrM 1096 C 1 a B +chrM 1097 A 1 , I +chrM 1098 A 1 , I +chrM 1099 A 1 , I +chrM 1100 A 1 , I +chrM 1101 T 1 , I +chrM 1102 G 2 ,^:, (I +chrM 1103 A 2 ,, II +chrM 1104 A 2 ,, I+ +chrM 1105 C 2 ,, .I +chrM 1106 A 2 ,, 8I diff -r ba2412c2a4d9 -r adff03258b45 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Sep 02 13:36:16 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 04 10:23:37 2009 -0400 @@ -339,5 +339,6 @@ <tool file="samtools/sam_to_bam.xml" /> <tool file="samtools/sam_merge.xml" /> <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> </section> </toolbox> diff -r ba2412c2a4d9 -r adff03258b45 tools/samtools/pileup_parser.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools/pileup_parser.pl Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,98 @@ +#! /usr/bin/perl -w + +use strict; + +die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file>\n" unless @ARGV == 11; + +my $in_file = $ARGV[0]; +my $ref_base_column = $ARGV[1]-1; # 1 based +my $read_bases_column = $ARGV[2]-1; # 1 based +my $base_quality_column = $ARGV[3]-1; # 1 based +my $cvrg_column = $ARGV[4]-1; # 1 based +my $quality_cutoff = $ARGV[5]; # phred scale integer +my $cvrg_cutoff = $ARGV[6]; # unsigned integer +my $SNPs_only = $ARGV[7]; # set to "Yes" to print only positions with SNPs; set to "No" to pring everything +my $bed = $ARGV[8]; #set to "Yes" to convert coordinates to bed format (0-based start, 1-based end); set to "No" to leave as is +my $coord_column = $ARGV[9]-1; #1 based +my $out_file = $ARGV[10]; + +my $invalid_line_counter = 0; +my $first_skipped_line = ""; +my %SNPs = ('A',0,'T',0,'C',0,'G',0); +my $above_qv_bases = 0; +my $SNPs_exist = 0; +my $out_string = ""; + +open (IN, "<$in_file") or die "Cannot open $in_file $!\n"; +open (OUT, ">$out_file") or die "Cannot open $out_file $!\n"; + +while (<IN>) { + chop; + my @fields = split /\t/; + next if $fields[ $ref_base_column ] eq "*"; # skip indel lines + next if $fields[ $cvrg_column ] < $cvrg_cutoff; # skip low coverage lines + my $read_bases = $fields[ $read_bases_column ]; + my $base_quality = $fields[ $base_quality_column ]; + + if ($read_bases =~ m/[\$\^\+-]/) { + $read_bases =~ s/\$//g; #removing end of the read segment mark + $read_bases =~ s/\^.//g; #removing the start of the read segement mark + while ($read_bases =~ m/[\+-]{1}(\d+)/g) { + my $indel_len = $1; + $read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field + } + } + if ( length($read_bases) != length($base_quality) ) { + + $first_skipped_line = $_ if $invalid_line_counter == 0; + ++$invalid_line_counter; + } + # after removing read block and indel data the length of read_base + # field should identical to the length of base_quality field + + my @bases = split //, $read_bases; + my @qv = split //, $base_quality; + + for my $base ( 0 .. @bases - 1 ) { + if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff ) + { + ++$above_qv_bases; + + if ( $bases[ $base ] =~ m/[ATGC]/i ) + { + $SNPs_exist = 1; + $SNPs{ uc( $bases[ $base ] ) } += 1; + } + } + } + + if ($bed eq "Yes") { + my $start = $fields[ $coord_column ] - 1; + my $end = $fields[ $coord_column ]; + $fields[ $coord_column ] = "$start\t$end"; + } + + $out_string = join("\t", @fields); # \t$read_bases\t$base_quality"; + foreach my $SNP (sort keys %SNPs) { + $out_string .= "\t$SNPs{$SNP}"; + } + $out_string .= "\t$above_qv_bases\n"; + + if ( $SNPs_only eq "Yes" ) { + print OUT $out_string if $SNPs_exist == 1; + } else { + print OUT $out_string; + } + + + %SNPs = (); + %SNPs = ('A',0,'T',0,'C',0,'G',0); + $above_qv_bases = 0; + $SNPs_exist = 0; + + +} + +print STDERR "Could not parse $invalid_line_counter line(s) beginning with: $first_skipped_line\n" if $invalid_line_counter > 0; +close IN; +close OUT; \ No newline at end of file diff -r ba2412c2a4d9 -r adff03258b45 tools/samtools/pileup_parser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools/pileup_parser.xml Fri Sep 04 10:23:37 2009 -0400 @@ -0,0 +1,286 @@ +<tool id="pileup_parser" name="Parse pileup"> + <description>to find variants</description> + <command interpreter="perl"> + #if $pileup_type.type_select == "six": #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 + #elif $pileup_type.type_select == "ten": #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 + #elif $pileup_type.type_select == "manual": #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 + #end if + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Select dataset"/> + <conditional name="pileup_type"> + <param name="type_select" type="select" label="which contains" help="See "Types of pileup datasets" below for examples"> + <option value="six" selected="true">Pileup with six columns (simple)</option> + <option value="ten">Pileup with ten columns (with consensus)</option> + <option value="manual">Set columns manually</option> + </param> + <when value="manual"> + <param name="ref_base_column" label="Select column with reference base" type="data_column" numerical="false" data_ref="input" /> + <param name="read_bases_column" label="Select column with read bases" type="data_column" numerical="false" data_ref="input" help="something like this: ..,a.."/> + <param name="read_qv_column" label="Select column with base qualities" type="data_column" numerical="false" data_ref="input" help="something like this: IIIGIAI"/> + <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" /> + <param name="coord_column" label="Select coordinate column" type="data_column" numerical="true" data_ref="input" /> + </when> + <when value="six"> + </when> + <when value="ten"> + </when> + </conditional> + <param name="qv_cutoff" label="Do not consider read bases with quality lower than" type="integer" value="20" help="No variants with quality below this value will be reported"/> + <param name="cvrg_cutoff" label="Do not report positions with coverage lower than" type="integer" value="3" help="Pileup lines with coverage lower than this value will be skipped"/> + <param name="snps_only" label="Only report variants?" type="select" help="See "Examples 1 and 2" below for explanation"> + <option value="No">No</option> + <option value="Yes" selected="true">Yes</option> + </param> + <param name="interval" label="Convert coordinates to intervals?" type="select" help="See "Output format" below for explanation"> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + + </inputs> + <outputs> + <data format="tabular" name="out_file1"> + <change_format> + <when input="interval" value="Yes" format="interval" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="pileup_parser.6col.pileup"/> + <output name="out_file1" file="pileup_parser.6col.20-3-yes-yes.pileup.out"/> + <param name="type_select" value="six"/> + <param name="qv_cutoff" value="20" /> + <param name="cvrg_cutoff" value="3" /> + <param name="snps_only" value="Yes"/> + <param name="interval" value="Yes" /> + </test> + <test> + <param name="input" value="pileup_parser.6col.pileup"/> + <output name="out_file1" file="pileup_parser.6col.20-3-yes-no.pileup.out"/> + <param name="type_select" value="six"/> + <param name="qv_cutoff" value="20" /> + <param name="cvrg_cutoff" value="3" /> + <param name="snps_only" value="Yes"/> + <param name="interval" value="No" /> + </test> + <test> + <param name="input" value="pileup_parser.6col.pileup"/> + <output name="out_file1" file="pileup_parser.6col.20-3-no-no.pileup.out"/> + <param name="type_select" value="six"/> + <param name="qv_cutoff" value="20" /> + <param name="cvrg_cutoff" value="3" /> + <param name="snps_only" value="No"/> + <param name="interval" value="No" /> + </test> + <test> + <param name="input" value="pileup_parser.10col.pileup"/> + <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/> + <param name="type_select" value="ten"/> + <param name="qv_cutoff" value="20" /> + <param name="cvrg_cutoff" value="3" /> + <param name="snps_only" value="Yes"/> + <param name="interval" value="Yes" /> + </test> + <test> + <param name="input" value="pileup_parser.10col.pileup"/> + <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/> + <param name="type_select" value="manual"/> + <param name="ref_base_column" value="3"/> + <param name="read_bases_column" value="9"/> + <param name="read_qv_column" value="10"/> + <param name="cvrg_column" value="8"/> + <param name="coord_column" value="2"/> + <param name="qv_cutoff" value="20" /> + <param name="cvrg_cutoff" value="3" /> + <param name="snps_only" value="Yes"/> + <param name="interval" value="Yes" /> + </test> + </tests> +<help> + +**What is does** + +Allows to find sequence variants and/or sites covered by specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following: + +- the quality scores follow phred33 convention, where input qualities are ASCII characters equal to the Phred quality plus 33. +- the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually). + +-------- + +**Types of pileup datasets** + +The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. + +.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml + +**Six column pileup**:: + + 1 2 3 4 5 6 + --------------------------------- + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Coverage (# reads aligning over that position) + 5 Bases within reads where (see Galaxy wiki for more info) + 6 Quality values (phred33 scale, see Galaxy wiki for more) + +**Ten column pileup** + +The `ten-column`__ pileup incoroporates additional consensus information generated with *-c* option of *samtools pileup* command:: + + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------ + chrM 412 A A 75 0 25 2 ., II + chrM 413 G G 72 0 25 4 ..t, IIIH + chrM 414 C C 75 0 25 4 ...a III2 + chrM 415 C T 75 75 25 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Consensus bases + 5 Consensus quality + 6 SNP quality + 7 Maximum mapping quality + 8 Coverage (# reads aligning over that position) + 9 Bases within reads where (see Galaxy wiki for more info) + 10 Quality values (phred33 scale, see Galaxy wiki for more) + + +.. __: http://samtools.sourceforge.net/cns0.shtml + +------ + +**The output format** + +The tool modifies the input dataset in two ways: +

1 0

[hg] galaxy 2661: More performance improvements in checking secu...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/99dcba7af5b6 changeset: 2661:99dcba7af5b6 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Sep 04 10:31:23 2009 -0400 description: More performance improvements in checking security on datasets and generatng HTML for libraries, and a bit of code cleanup in these areas. 30 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0017_library_item_indexes.py lib/galaxy/security/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/parameters/basic.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/__init__.py templates/admin/library/browse_library.mako templates/admin/library/common.mako templates/admin/library/ldda_info.mako templates/dataset/edit_attributes.mako templates/library/browse_library.mako templates/library/common.mako templates/library/folder_info.mako templates/library/folder_permissions.mako templates/library/ldda_edit_info.mako templates/library/ldda_info.mako templates/library/library_dataset_info.mako templates/library/library_dataset_permissions.mako templates/library/library_info.mako templates/library/library_permissions.mako templates/mobile/history/detail.mako templates/mobile/manage_library.mako templates/root/history_common.mako diffs (1594 lines): diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/model/__init__.py Fri Sep 04 10:31:23 2009 -0400 @@ -709,9 +709,9 @@ folder.order_id = self.item_count self.item_count += 1 def get_info_association( self, restrict=False ): - # If restrict is True, we will return this folder's info_association whether it - # exists or not. If restrict is False, we'll return the next available info_association - # in the inheritable hierarchy + # If restrict is True, we will return this folder's info_association, not inheriting. + # If restrict is False, we'll return the next available info_association in the + # inheritable hierarchy if self.info_association: return self.info_association[0] if restrict: @@ -721,9 +721,6 @@ if self.library_root: return self.library_root[0].get_info_association() return None - @property - def active_components( self ): - return list( self.active_folders ) + list( self.active_library_datasets ) @property def active_library_datasets( self ): # This needs to be a list @@ -736,10 +733,6 @@ def active_datasets( self ): # This needs to be a list return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] - @property #make this a relation - def activatable_folders( self ): - # This needs to be a list - return [ folder for folder in self.folders if not folder.purged ] class LibraryDataset( object ): # This class acts as a proxy to the currently selected LDDA @@ -1062,17 +1055,11 @@ return s return False def submitted(self): - if self.state == self.states.SUBMITTED: - return True - return False + return self.state == self.states.SUBMITTED def unsubmitted(self): - if self.state == self.states.UNSUBMITTED: - return True - return False + return self.state == self.states.UNSUBMITTED def complete(self): - if self.state == self.states.COMPLETE: - return True - return False + return self.state == self.states.COMPLETE class RequestType( object ): def __init__(self, name=None, desc=None, request_form=None, sample_form=None): diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri Sep 04 10:31:23 2009 -0400 @@ -233,10 +233,10 @@ Column( "id", Integer, primary_key=True ), Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), - Column( "order_id", Integer ), + Column( "order_id", Integer ), #not currently being used, but for possible future use Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "name", TrimmedString( 255 ), key="_name" ), #when not None/null this will supercede display in library (but not when imported into user's history?) + Column( "name", TrimmedString( 255 ), key="_name", index=True ), #when not None/null this will supercede display in library (but not when imported into user's history?) Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) Column( "deleted", Boolean, index=True, default=False ) ) @@ -248,7 +248,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ), Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ), - Column( "name", TrimmedString( 255 ) ), + Column( "name", TrimmedString( 255 ), index=True ), Column( "info", TrimmedString( 255 ) ), Column( "blurb", TrimmedString( 255 ) ), Column( "peek" , TEXT ), @@ -276,9 +276,9 @@ Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "name", TEXT ), + Column( "name", TEXT, index=True ), Column( "description", TEXT ), - Column( "order_id", Integer ), + Column( "order_id", Integer ), #not currently being used, but for possible future use Column( "item_count", Integer ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), @@ -823,15 +823,16 @@ folders=relation( LibraryFolder, primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), + order_by=asc( LibraryFolder.table.c.name ), backref=backref( "parent", primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), remote_side=[LibraryFolder.table.c.id] ) ), active_folders=relation( LibraryFolder, primaryjoin=( ( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolder.table.c.deleted ) ) ), - order_by=asc( LibraryFolder.table.c.order_id ), + order_by=asc( LibraryFolder.table.c.name ), lazy=True, #"""sqlalchemy.exceptions.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship.""" viewonly=True ), datasets=relation( LibraryDataset, primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ), - order_by=asc( LibraryDataset.table.c.order_id ), + order_by=asc( LibraryDataset.table.c._name ), lazy=False, viewonly=True ) ) ) diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/model/migrate/versions/0017_library_item_indexes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Fri Sep 04 10:31:23 2009 -0400 @@ -0,0 +1,53 @@ +""" +This script adds 3 indexes to table columns: library_folder.name, +library_dataset.name, library_dataset_dataset_association.name. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) +LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) +LibraryDataset_table = Table( "library_dataset", metadata, autoload=True ) + +def display_migration_details(): + print "========================================" + print "This script adds 3 indexes to table columns: library_folder.name," + print "library_dataset.name, library_dataset_dataset_association.name." + print "========================================" + +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + # Add 1 index to the library_folder table + i = Index( 'ix_library_folder_name', LibraryFolder_table.c.name ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_library_folder_name' to library_folder table failed: %s" % ( str( e ) ) ) + # Add 1 index to the library_dataset_dataset_association table + i = Index( 'ix_library_dataset_dataset_association_name', LibraryDatasetDatasetAssociation_table.c.name ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_library_dataset_dataset_association_name' to library_dataset_dataset_association table failed: %s" % ( str( e ) ) ) + # Add 1 index to the library_dataset table + i = Index( 'ix_library_dataset_name', LibraryDataset_table.c.name ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_library_dataset_name' to library_dataset table failed: %s" % ( str( e ) ) ) +def downgrade(): + log.debug( "Downgrade is not possible." ) diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/security/__init__.py Fri Sep 04 10:31:23 2009 -0400 @@ -33,11 +33,19 @@ def get_actions( self ): """Get all permitted actions as a list of Action objects""" return self.permitted_actions.__dict__.values() - def allow_action( self, user, roles, action, **kwd ): - raise 'No valid method of checking action (%s) on %s for user %s.' % ( action, kwd, user ) def get_item_action( self, action, item ): raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) def guess_derived_permissions_for_datasets( self, datasets = [] ): + raise "Unimplemented Method" + def can_access_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_manage_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_add_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_modify_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_manage_library_item( self, user, roles, item ): raise "Unimplemented Method" def associate_components( self, **kwd ): raise 'No valid method of associating provided components: %s' % kwd @@ -89,36 +97,20 @@ to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.model.context.current - def allow_action( self, user, roles, action, **kwd ): - if 'dataset' in kwd: - return self.allow_dataset_action( user, roles, action, kwd[ 'dataset' ] ) - elif 'library_item' in kwd: - return self.allow_library_item_action( user, roles, action, kwd[ 'library_item' ] ) - raise 'No valid method of checking action (%s) for user %s using kwd %s' % ( action, str( user ), str( kwd ) ) - def allow_dataset_action( self, user, roles, action, dataset ): - """Returns true when user has permission to perform an action""" - if not user: - if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in dataset.actions ]: - # anons only get access, and only if there are no roles required for the access action - # Other actions (or if the dataset has roles defined for the access action) fall through - # to the false below for anons - return True - elif action.action not in [ dp.action for dp in dataset.actions ]: - if action.model == 'restrict': - # Implicit access to restrict-style actions if the dataset does not have the action - # Grant style actions fall through to the false below - return True - else: - perms = self.get_dataset_permissions( dataset ) - if action in perms.keys(): - # The filter() returns a list of the dataset's role ids of which the user is not a member, - # so an empty list means the user has all of the required roles. - if not filter( lambda x: x not in roles, [ r for r in perms[ action ] ] ): - # User has all of the roles required to perform the action - return True - # The user is missing at least one required role - return False - def allow_library_item_action( self, user, roles, action, library_item ): + def allow_dataset_action( self, roles, action, dataset ): + """ + Returns true when user has permission to perform an action on an + instance of Dataset. + """ + dataset_action = self.get_item_action( action, dataset ) + if dataset_action is None: + return action.model == 'restrict' + return dataset_action.role in roles + def can_access_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset ) + def can_manage_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) + def allow_library_item_action( self, user, roles, action, item ): """ Method for checking a permission for the current user to perform a specific library action on a library item, which must be one of: @@ -127,30 +119,22 @@ if user is None: # All permissions are granted, so non-users cannot have permissions return False - # Check to see if user has access to any of the roles - allowed_role_assocs = [] - for item_class, permission_class in self.library_item_assocs: - if isinstance( library_item, item_class ): - if permission_class == self.model.LibraryPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, - library=library_item ).all() - elif permission_class == self.model.LibraryFolderPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, - folder=library_item ).all() - elif permission_class == self.model.LibraryDatasetPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, - library_dataset=library_item ).all() - elif permission_class == self.model.LibraryDatasetDatasetAssociationPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, - library_dataset_dataset_association=library_item ).all() - for allowed_role_assoc in allowed_role_assocs: - if allowed_role_assoc.role in roles: - return True - return False + # Check to see if user has access to any of the roles associated with action + item_action = self.get_item_action( action, item ) + if item_action is None: + # All permissions are granted, so item must have action + return False + return item_action.role in roles + def can_add_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item ) + def can_modify_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item ) + def can_manage_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item ) def get_item_action( self, action, item ): # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation for permission in item.actions: - if permission.action == action: + if permission.action == action.action: return permission return None def guess_derived_permissions_for_datasets( self, datasets=[] ): @@ -282,10 +266,7 @@ if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]: # Don't change permissions on a dataset associated with a history not owned by the user continue - if bypass_manage_permission or self.allow_action( user, - user.all_roles(), - self.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=dataset ): + if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ): self.set_all_dataset_permissions( dataset, permissions ) def history_get_default_permissions( self, history ): permissions = {} @@ -445,7 +426,7 @@ the string, True is returned if the current user has permission to perform any 1 of actions_to_check on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets this criteria, if it exists. - """ + """ for action in actions_to_check: if self.allow_library_item_action( user, roles, action, library_item ): return True, hidden_folder_ids @@ -515,7 +496,7 @@ with the string, True is returned if the current user has permission to access folder. Otherwise, cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. """ - action = self.permitted_actions.DATASET_ACCESS.action + action = self.permitted_actions.DATASET_ACCESS lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ .join( "library_dataset" ) \ .filter( self.model.LibraryDataset.folder == folder ) \ diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Fri Sep 04 10:31:23 2009 -0400 @@ -48,10 +48,7 @@ assoc.flush() data = new_data user, roles = trans.get_user_and_roles() - if data and not trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset=data.dataset ): + if data and not trans.app.security_agent.can_access_dataset( roles, data.dataset ): raise "User does not have permission to use a dataset (%s) provided for input." % data.id return data if isinstance( input, DataToolParameter ): @@ -267,10 +264,7 @@ user, roles = trans.get_user_and_roles() for name, dataset in inp_data.iteritems(): if dataset: - if not trans.app.security_agent.allow_action( user, - roles, - dataset.permitted_actions.DATASET_ACCESS, - dataset=dataset.dataset ): + if not trans.app.security_agent.can_access_dataset( roles, dataset.dataset ): raise "User does not have permission to use a dataset (%s) provided for input." % data.id job.add_input_dataset( name, dataset ) else: diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Sep 04 10:31:23 2009 -0400 @@ -1149,19 +1149,11 @@ hid = str( hda.hid ) if not hda.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED] and \ hda.visible and \ - trans.app.security_agent.allow_action( user, - roles, - hda.permitted_actions.DATASET_ACCESS, - dataset=hda.dataset ): + trans.app.security_agent.can_access_dataset( roles, hda.dataset ): # If we are sending data to an external application, then we need to make sure there are no roles - # associated with the dataset that restrict it's access from "public". We determine this by sending - # None as the user to the allow_action method. - if self.tool and self.tool.tool_type == 'data_destination': - if not trans.app.security_agent.allow_action( None, - None, - hda.permitted_actions.DATASET_ACCESS, - dataset=hda.dataset ): - continue + # associated with the dataset that restrict it's access from "public". + if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ): + continue if self.options and hda.get_dbkey() != filter_value: continue if isinstance( hda.datatype, self.formats): @@ -1172,10 +1164,7 @@ if target_ext: if converted_dataset: hda = converted_dataset - if not trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset=hda.dataset ): + if not trans.app.security_agent.can_access_dataset( roles, hda.dataset ): continue selected = ( value and ( hda in value ) ) field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Sep 04 10:31:23 2009 -0400 @@ -2001,7 +2001,6 @@ show_deleted=False, msg=msg, messagetype=messagetype ) - def _save_request_type(self, trans, **kwd): params = util.Params( kwd ) num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) @@ -2031,7 +2030,6 @@ ss.flush() msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) return rt, msg - @web.expose @web.require_admin def delete_request_type( self, trans, **kwd ): @@ -2045,7 +2043,6 @@ action='manage_request_types', msg='Request type <b>%s</b> has been deleted' % rt.name, messagetype='done') ) - @web.expose @web.require_admin def undelete_request_type( self, trans, **kwd ): diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Sep 04 10:31:23 2009 -0400 @@ -109,10 +109,7 @@ if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset=data.dataset ): + if trans.app.security_agent.can_access_dataset( roles, data.dataset ): if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) if filename is None or filename.lower() == "index": @@ -147,12 +144,9 @@ return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( None, None, data.permitted_actions.DATASET_ACCESS, dataset=data.dataset ): + if trans.app.security_agent.dataset_is_public( data.dataset ): return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac - if trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset=data.dataset ): + if trans.app.security_agent.can_access_dataset( roles, data.dataset ): trans.app.host_security_agent.set_dataset_permissions( data, trans.user, site ) return trans.response.send_redirect( redirect_url ) else: diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Sep 04 10:31:23 2009 -0400 @@ -443,15 +443,9 @@ for hda in history.activatable_datasets: # If the current dataset is not public, we may need to perform an action on it to # make it accessible by the other user. - if not trans.app.security_agent.allow_action( send_to_user, - send_to_user.all_roles(), - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset=hda.dataset ): + if not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ): # The user with which we are sharing the history does not have access permission on the current dataset - if trans.app.security_agent.allow_action( user, - user_roles, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=hda.dataset ) and not hda.dataset.library_associations: + if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations: # The current user has authority to change permissions on the current dataset because # they have permission to manage permissions on the dataset and the dataset is not associated # with a library. @@ -556,15 +550,9 @@ no_change_needed[ send_to_user ][ history ] = [ hda ] else: no_change_needed[ send_to_user ][ history ].append( hda ) - elif not trans.app.security_agent.allow_action( send_to_user, - send_to_user.all_roles(), - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset=hda.dataset ): + elif not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ): # The user with which we are sharing the history does not have access permission on the current dataset - if trans.app.security_agent.allow_action( user, - user_roles, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=hda.dataset ) and not hda.dataset.library_associations: + if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations: # The current user has authority to change permissions on the current dataset because # they have permission to manage permissions on the dataset and the dataset is not associated # with a library. diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Fri Sep 04 10:31:23 2009 -0400 @@ -2,6 +2,7 @@ from galaxy.model.orm import * from galaxy.datatypes import sniff from galaxy import util +from galaxy.util.odict import odict from galaxy.web.controllers.forms import get_all_forms, get_form_widgets from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys @@ -74,7 +75,7 @@ # The folders that should not be displayed may not be a complete list, but it is ultimately passed # to the browse_library() method and the browse_library.mako template to keep from re-checking the # same folders when the library is rendered. - authorized_libraries = {} + authorized_libraries = odict() for library in all_libraries: can_access, hidden_folder_ids = trans.app.security_agent.check_folder_contents( user, roles, library.root_folder ) if can_access: @@ -283,10 +284,7 @@ user, roles = trans.get_user_and_roles() for id in ldda_ids: ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda or not trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset = ldda.dataset ): + if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ): continue path = "" parent_folder = ldda.library_dataset.folder @@ -384,10 +382,7 @@ user, roles = trans.get_user_and_roles() if action == 'information': if params.get( 'edit_attributes_button', False ): - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=library_dataset ): + if trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ): if params.get( 'edit_attributes_button', False ): old_name = library_dataset.name new_name = util.restore_text( params.get( 'name', '' ) ) @@ -411,10 +406,7 @@ messagetype=messagetype ) elif action == 'permissions': if params.get( 'update_roles_button', False ): - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=library_dataset ): + if trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ): # The user clicked the Save button on the 'Associate With Roles' form permissions = {} for k, v in trans.app.model.Library.permitted_actions.items(): @@ -501,14 +493,8 @@ if action == 'permissions': if params.get( 'update_roles_button', False ): # The user clicked the Save button on the 'Associate With Roles' form - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=ldda ) and \ - trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=ldda.dataset ): + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] @@ -547,10 +533,7 @@ elif action == 'edit_info': if params.get( 'change', False ): # The user clicked the Save button on the 'Change data type' form - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=ldda ): + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) trans.app.model.flush() @@ -571,10 +554,7 @@ messagetype=messagetype ) elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=ldda ): + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): old_name = ldda.name new_name = util.restore_text( params.get( 'name', '' ) ) new_info = util.restore_text( params.get( 'info', '' ) ) @@ -613,10 +593,7 @@ messagetype=messagetype ) elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=ldda ): + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): for name, spec in ldda.datatype.metadata_spec.items(): # We need to be careful about the attributes we are resetting if name not in [ 'name', 'info', 'dbkey' ]: @@ -638,10 +615,7 @@ msg=msg, messagetype=messagetype ) elif params.get( 'delete', False ): - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=folder ): + if trans.app.security_agent.can_modify_library_item( user, roles, folder ): ldda.deleted = True ldda.flush() msg = 'Dataset %s has been removed from this library' % ldda.name @@ -656,10 +630,7 @@ widgets=widgets, msg=msg, messagetype=messagetype ) - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=ldda ): + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): ldda.datatype.before_edit( ldda ) if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability @@ -697,14 +668,8 @@ messagetype='error' ) ) if action == 'permissions': if params.get( 'update_roles_button', False ): - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=ldda ) and \ - trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=ldda.dataset ): + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] @@ -735,14 +700,8 @@ library_id=library_id, msg=msg, messagetype=messagetype ) - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=ldda ) and \ - trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=ldda.dataset ): + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): # Ensure that the permissions across all library items are identical, otherwise we can't update them together. check_list = [] for ldda in lddas: @@ -774,14 +733,8 @@ library_id=library_id, msg=msg, messagetype=messagetype ) - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_ADD, - library_item=folder ) or \ - ( replace_dataset and trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=replace_dataset ) ): + if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \ + ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ): if params.get( 'new_dataset_button', False ): upload_option = params.get( 'upload_option', 'upload_file' ) created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, @@ -804,10 +757,7 @@ # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need # to check one of them to see if the current user can manage permissions on them. check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] ) - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=check_ldda ): + if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ): if replace_dataset: default_action = '' else: @@ -929,10 +879,7 @@ # to check one of them to see if the current user can manage permissions on them. check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] ) user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=check_ldda ): + if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ): if replace_dataset: default_action = '' else: @@ -1033,10 +980,7 @@ else: widgets = [] if params.get( 'rename_folder_button', False ): - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=folder ): + if trans.app.security_agent.can_modify_library_item( user, roles, folder ): old_name = folder.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) @@ -1077,10 +1021,7 @@ elif action == 'permissions': if params.get( 'update_roles_button', False ): # The user clicked the Save button on the 'Associate With Roles' form - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=folder ): + if trans.app.security_agent.can_manage_library_item( user, roles, folder ): permissions = {} for k, v in trans.app.model.Library.permitted_actions.items(): in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ] @@ -1202,3 +1143,41 @@ edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) + +# ---- Utility methods ------------------------------------------------------- + +def active_folders( trans, folder ): + # Much faster way of retrieving all active sub-folders within a given folder than the + # performance of the mapper. This query also eagerloads the permissions on each folder. + return trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .filter_by( parent=folder, deleted=False ) \ + .options( eagerload_all( "actions" ) ) \ + .order_by( trans.app.model.LibraryFolder.table.c.name ) \ + .all() +def activatable_folders( trans, folder ): + return trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .filter_by( parent=folder, purged=False ) \ + .options( eagerload_all( "actions" ) ) \ + .order_by( trans.app.model.LibraryFolder.table.c.name ) \ + .all() +def active_folders_and_lddas( trans, folder ): + folders = active_folders( trans, folder ) + # This query is much faster than the folder.active_library_datasets property + lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ + .filter_by( deleted=False ) \ + .join( "library_dataset" ) \ + .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ + .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ + .all() + return folders, lddas +def activatable_folders_and_lddas( trans, folder ): + folders = activatable_folders( trans, folder ) + # This query is much faster than the folder.activatable_library_datasets property + lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ + .join( "library_dataset" ) \ + .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ + .join( "dataset" ) \ + .filter( trans.app.model.Dataset.table.c.deleted==False ) \ + .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ + .all() + return folders, lddas diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Fri Sep 04 10:31:23 2009 -0400 @@ -4,6 +4,7 @@ from galaxy.datatypes import sniff from galaxy import util from galaxy.util.streamball import StreamBall +from galaxy.util.odict import odict import logging, tempfile, zipfile, tarfile, os, sys from galaxy.web.form_builder import * from datetime import datetime, timedelta @@ -470,7 +471,7 @@ # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids # so that you do not need to check those same folders yet again when populating the select list. # - libraries = {} + libraries = odict() for library in all_libraries: can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) if can_show: diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri Sep 04 10:31:23 2009 -0400 @@ -153,10 +153,7 @@ return "Dataset id '%s' is invalid" %str( id ) if data: user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset = data.dataset ): + if trans.app.security_agent.can_access_dataset( roles, data.dataset ): mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) if tofile: @@ -189,10 +186,7 @@ child = data.get_child_by_designation( designation ) if child: user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( user, - roles, - child.permitted_actions.DATASET_ACCESS, - dataset = child ): + if trans.app.security_agent.can_access_dataset( roles, child ): return self.display( trans, id=child.id, tofile=tofile, toext=toext ) else: return "You are not privileged to access this dataset." @@ -209,10 +203,7 @@ authz_method = kwd['authz_method'] if data: user, roles = trans.get_user_and_roles() - if authz_method == 'rbac' and trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset = data ): + if authz_method == 'rbac' and trans.app.security_agent.can_access_dataset( roles, data ): trans.response.set_content_type( data.get_mime() ) trans.log_event( "Formatted dataset id %s for display at %s" % ( str( id ), display_app ) ) return data.as_display_type( display_app, **kwd ) @@ -262,10 +253,7 @@ if id is not None and data.history.user is not None and data.history.user != trans.user: return trans.show_error_message( "This instance of a dataset (%s) in a history does not belong to you." % ( data.id ) ) user, roles = trans.get_user_and_roles() - if trans.app.security_agent.allow_action( user, - roles, - data.permitted_actions.DATASET_ACCESS, - dataset=data.dataset ): + if trans.app.security_agent.can_access_dataset( roles, data.dataset ): if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." ) params = util.Params( kwd, safe=False ) @@ -331,10 +319,7 @@ elif params.update_roles_button: if not trans.user: return trans.show_error_message( "You must be logged in if you want to change permissions." ) - if trans.app.security_agent.allow_action( user, - roles, - data.dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset = data.dataset ): + if trans.app.security_agent.can_manage_dataset( roles, data.dataset ): permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): in_roles = params.get( k + '_in', [] ) diff -r adff03258b45 -r 99dcba7af5b6 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Sep 04 10:23:37 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Sep 04 10:31:23 2009 -0400 @@ -503,7 +503,7 @@ if user: roles = user.all_roles() else: - roles = None + roles = [] return user, roles def user_is_admin( self ): diff -r adff03258b45 -r 99dcba7af5b6 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/admin/library/browse_library.mako Fri Sep 04 10:31:23 2009 -0400 @@ -1,17 +1,15 @@ <%inherit file="/base.mako"/> -<%namespace file="common.mako" import="render_dataset" /> <%namespace file="/message.mako" import="render_msg" /> -<% from galaxy import util %> +<% + from time import strftime + from galaxy import util + from galaxy.web.controllers.library import active_folders_and_lddas, activatable_folders_and_lddas +%> <%def name="stylesheets()"> <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> <link href="${h.url_for('/static/style/library.css')}" rel="stylesheet" type="text/css" /> </%def> - -<% -def name_sorted( l ): - return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) ) -%> <script type="text/javascript"> $( document ).ready( function () { @@ -72,24 +70,77 @@ } </script> -<%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id )"> +<%def name="render_dataset( ldda, library_dataset, selected, library, folder, deleted, show_deleted )"> <% - root_folder = not folder.parent + ## The received data must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods + ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying + ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this + ## library_dataset, so we display the attributes from the ldda. + if ldda.user: + uploaded_by = ldda.user.email + else: + uploaded_by = 'anonymous' + if ldda == library_dataset.library_dataset_dataset_association: + current_version = True + else: + current_version = False + %> + <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}"> + ## Header row for library items (name, state, action buttons) + <div class="historyItemTitleBar"> + <table cellspacing="0" cellpadding="0" border="0" width="100%"> + <tr> + <td width="*"> + %if selected: + <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> + %else: + <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> + %endif + <span class="libraryItemDeleted-${ldda.deleted}"> + <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> + </span> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + %if not library.deleted and not folder.deleted and not library_dataset.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use + ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + %if current_version: + <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + %endif + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + %endif + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> + </div> + %elif not library.deleted and not folder.deleted and library_dataset.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> + </div> + %endif + </td> + <td width="300">${ldda.message}</td> + <td width="150">${uploaded_by}</td> + <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + </tr> + </table> + </div> + </div> +</%def> + +<%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id, root_folder=False )"> + <% if root_folder: pad = folder_pad + expander = "/static/images/silk/resultset_bottom.png" + folder_img = "/static/images/silk/folder_page.png" else: pad = folder_pad + 20 - if folder_pad == 0: - expander = "/static/images/silk/resultset_bottom.png" - folder_img = "/static/images/silk/folder_page.png" - subfolder = False - else: expander = "/static/images/silk/resultset_next.png" folder_img = "/static/images/silk/folder.png" - subfolder = True - created_ldda_id_list = util.listify( created_ldda_ids ) - if created_ldda_id_list: - created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ] + if created_ldda_ids: + created_ldda_ids = [ int( ldda_id ) for ldda_id in util.listify( created_ldda_ids ) ] %> %if not root_folder: <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"> @@ -104,10 +155,6 @@ </div> %endif %if not folder.deleted: - <% - library_item_ids = {} - library_item_ids[ 'folder' ] = folder.id - %> <div popupmenu="folder-${folder.id}-popup"> <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> @@ -130,30 +177,31 @@ %endif </li> %endif - %if subfolder: + %if pad > 0: <ul id="subFolder"> %else: <ul> %endif %if show_deleted: <% - parent_folders = folder.activatable_folders - parent_datasets = folder.activatable_library_datasets + sub_folders, lddas = activatable_folders_and_lddas( trans, folder ) %> %else: <% - parent_folders = folder.active_folders - parent_datasets = folder.active_library_datasets + sub_folders, lddas = active_folders_and_lddas( trans, folder ) %> %endif - %for folder in name_sorted( parent_folders ): - ${render_folder( folder, pad, deleted, show_deleted, created_ldda_ids, library_id )} - %endfor - %for library_dataset in name_sorted( parent_datasets ): + %for sub_folder in sub_folders: + ${render_folder( sub_folder, pad, deleted, show_deleted, created_ldda_ids, library_id )} + %endfor + %for ldda in lddas: <% - selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids + library_dataset = ldda.library_dataset + selected = created_ldda_ids and ldda.id in created_ldda_ids %> - <li class="datasetRow" style="padding-left: ${pad + 18}px;">${render_dataset( library_dataset, selected, library, deleted, show_deleted )}</li> + <li class="datasetRow" style="padding-left: ${pad + 18}px;"> + ${render_dataset( ldda, library_dataset, selected, library, folder, deleted, show_deleted )} + </li> %endfor </ul> </%def> @@ -196,10 +244,6 @@ <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> %if not deleted: - <% - library_item_ids = {} - library_item_ids[ 'library' ] = library.id - %> <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this data library's information</a> ## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition ##%if library.info_association: @@ -228,7 +272,7 @@ </div> </li> <ul> - ${render_folder( library.root_folder, 0, deleted, show_deleted, created_ldda_ids, library.id )} + ${render_folder( library.root_folder, 0, deleted, show_deleted, created_ldda_ids, library.id, root_folder=True )} </ul> <br/> </ul> diff -r adff03258b45 -r 99dcba7af5b6 templates/admin/library/common.mako --- a/templates/admin/library/common.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/admin/library/common.mako Fri Sep 04 10:31:23 2009 -0400 @@ -1,68 +1,3 @@ -<% from time import strftime %> - -<%def name="render_dataset( library_dataset, selected, library, deleted, show_deleted )"> - <% - ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu - ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always - ## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes - ## from the ldda. - ldda = library_dataset.library_dataset_dataset_association - if ldda.user: - uploaded_by = ldda.user.email - else: - uploaded_by = 'anonymous' - if ldda == ldda.library_dataset.library_dataset_dataset_association: - current_version = True - else: - current_version = False - %> - <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}"> - ## Header row for library items (name, state, action buttons) - <div class="historyItemTitleBar"> - <table cellspacing="0" cellpadding="0" border="0" width="100%"> - <tr> - <td width="*"> - %if selected: - <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> - %else: - <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> - %endif - <span class="libraryItemDeleted-${library_dataset.deleted}"> - <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> - </span> - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - %if not library.deleted and not library_dataset.folder.deleted and not library_dataset.deleted: - <% - library_item_ids = {} - library_item_ids[ 'ldda' ] = ldda.id - %> - <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> - ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use - ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> - %if current_version: - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> - %endif - %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> - %endif - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> - </div> - %elif not library.deleted and not library_dataset.folder.deleted and library_dataset.deleted: - <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> - </div> - %endif - </td> - <td width="300">${ldda.message}</td> - <td width="150">${uploaded_by}</td> - <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td> - </tr> - </table> - </div> - </div> -</%def> <%def name="render_template_info( library_item, library_id, widgets, editable=True )"> <% diff -r adff03258b45 -r 99dcba7af5b6 templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -86,26 +86,14 @@ <div class="form-row"> <div>${ldda.blurb}</div> </div> - <div class="form-row"> - <div id="info${ldda.id}" class="historyItemBody"> - %if ldda.peek != "no peek": + %if ldda.peek != "no peek": + <div class="form-row"> + <div id="info${ldda.id}" class="historyItemBody"> <label>Peek:</label> <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div> - %endif - ## Recurse for child datasets - %if len( ldda.visible_children ) > 0: - <div> - There are ${len( ldda.visible_children )} secondary datasets. - %for idx, child in enumerate( ldda.visible_children ): - ## TODO: do we need to clarify if the child is deleted? - %if not child.purged: - ${ render_dataset( child, selected, library, False, False ) } - %endif - %endfor - </div> - %endif + </div> </div> - </div> + %endif </div> %if widgets: ${render_template_info( ldda, library.id, widgets, editable=False )} diff -r adff03258b45 -r 99dcba7af5b6 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Fri Sep 04 10:31:23 2009 -0400 @@ -190,7 +190,7 @@ </div> <p /> -%if trans.app.security_agent.allow_action( user, user_roles, data.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=data.dataset ): +%if trans.app.security_agent.can_manage_dataset( user_roles, data.dataset ): <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> ${render_permission_form( data.dataset, data.name, h.url_for( controller='root', action='edit', id=data.id ), user_roles )} %elif trans.user: diff -r adff03258b45 -r 99dcba7af5b6 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/browse_library.mako Fri Sep 04 10:31:23 2009 -0400 @@ -2,6 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> <% from galaxy import util + from galaxy.web.controllers.library import active_folders from time import strftime user, roles = trans.get_user_and_roles() %> @@ -13,10 +14,6 @@ </%def> <% - -def name_sorted( l ): - return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) ) - class RowCounter( object ): def __init__( self ): self.count = 0 @@ -82,21 +79,22 @@ }); </script> -<%def name="render_dataset( library_dataset, selected, library, pad, parent, row_conter )"> +<%def name="render_dataset( ldda, library_dataset, selected, library, folder, pad, parent, row_conter )"> <% - ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu - ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always - ## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes + ## The id passed to methods from the drop down menu should be the ldda id to prevent id collision + ## ( which could happen when displaying children, which are always lddas ). We also need to make + ## sure we're displaying the latest version of this library_dataset, so we display the attributes ## from the ldda. - ldda = library_dataset.library_dataset_dataset_association if ldda.user: uploaded_by = ldda.user.email else: uploaded_by = 'anonymous' - if ldda == ldda.library_dataset.library_dataset_dataset_association: + if ldda == library_dataset.library_dataset_dataset_association: current_version = True else: current_version = False + can_modify_library_dataset = trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ) + can_manage_library_dataset = trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ) %> <tr class="datasetRow" @@ -111,19 +109,19 @@ %else: <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> %endif - <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> + <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + %if can_modify_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> %else: - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a> + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, information=True )}">View this dataset's information</a> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ): - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> - %if current_version and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + %if can_manage_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> %endif + %if current_version and can_modify_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> %endif %if ldda.has_data: <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> @@ -141,7 +139,7 @@ %> </%def> -<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None )"> +<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None, root_folder=False )"> <% if str( folder.id ) in hidden_folder_ids: return "" @@ -156,18 +154,15 @@ trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] ) if not can_show: return "" - root_folder = not folder.parent if root_folder: pad = folder_pad else: pad = folder_pad + 20 - if folder_pad == 0: - subfolder = False - else: - subfolder = True - created_ldda_id_list = util.listify( created_ldda_ids ) - if created_ldda_id_list: - created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ] + if created_ldda_ids: + created_ldda_ids = [ int( ldda_id ) for ldda_id in util.listify( created_ldda_ids ) ] + can_add = trans.app.security_agent.can_add_library_item( user, roles, folder ) + can_modify = trans.app.security_agent.can_modify_library_item( user, roles, folder ) + can_manage = trans.app.security_agent.can_manage_library_item( user, roles, folder ) my_row = None %> %if not root_folder: @@ -187,21 +182,19 @@ %endif <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="folder_img-${folder.id}-popup"> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): + %if can_add: <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): + %if can_modify: <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> %else: <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a> %endif - %if forms and not folder.info_association: - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this folder</a> - %endif + %if can_add and forms and not folder.info_association: + <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this folder</a> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ): + %if can_manage: <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> %endif </div> @@ -213,43 +206,48 @@ row_counter.increment() %> %endif - %for child_folder in name_sorted( folder.active_folders ): - ${render_folder( child_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, my_row, row_counter )} + <% sub_folders = active_folders( trans, folder ) %> + %for sub_folder in sub_folders: + ${render_folder( sub_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, parent=my_row, row_counter=row_counter )} %endfor - %for library_dataset in name_sorted( folder.active_library_datasets ): + %for library_dataset in folder.active_library_datasets: <% - selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids + ldda = library_dataset.library_dataset_dataset_association + can_access = trans.app.security_agent.can_access_dataset( roles, ldda.dataset ) + selected = created_ldda_ids and ldda.id in created_ldda_ids %> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ): - ${render_dataset( library_dataset, selected, library, pad, my_row, row_counter )} + %if can_access: + ${render_dataset( ldda, library_dataset, selected, library, folder, pad, my_row, row_counter )} %endif %endfor </%def> <h2>Data Library “${library.name}”</h2> +<% +can_add = trans.app.security_agent.can_add_library_item( user, roles, library ) +can_modify = trans.app.security_agent.can_modify_library_item( user, roles, library ) +can_manage = trans.app.security_agent.can_manage_library_item( user, roles, library ) +%> + <ul class="manage-table-actions"> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - %if not deleted: - <li> - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> - </li> - %endif + %if can_add and not_deleted: + <li> + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> + </li> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): + %if can_modify: <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a></li> %else: <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li> %endif - %if forms and not library.info_association: - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a> - %endif + %if can_add and forms and not library.info_association: + <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): + %if can_manage: <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li> %endif </ul> @@ -259,10 +257,6 @@ %endif <form name="import_from_library" action="${h.url_for( controller='library', action='datasets', library_id=library.id )}" method="post"> - <% - library_item_ids = {} - library_item_ids[ 'library' ] = library.id - %> <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> <thead> <tr class="libraryTitle"> @@ -273,7 +267,7 @@ </thead> </tr> <% row_counter = RowCounter() %> - ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, hidden_folder_ids, None, row_counter )} + ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, hidden_folder_ids, parent=None, row_counter=row_counter, root_folder=True )} <tfoot> <tr> <td colspan="4" style="padding-left: 42px;"> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/common.mako --- a/templates/library/common.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/common.mako Fri Sep 04 10:31:23 2009 -0400 @@ -21,7 +21,7 @@ <div class="toolForm"> <div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div> <div class="toolFormBody"> - %if editable and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library_item ): + %if editable and trans.app.security_agent.can_modify_library_item( user, roles, library_item ): <form name="edit_info" action="${h.url_for( controller='library', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post"> <input type="hidden" name="library_item_id" value="${library_item.id}"/> <input type="hidden" name="library_item_type" value="${library_item_type}"/> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/folder_info.mako --- a/templates/library/folder_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/folder_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -18,7 +18,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit folder name and description</div> <div class="toolFormBody"> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): + %if trans.app.security_agent.can_modify_library_item( user, roles, folder ): <form name="folder" action="${h.url_for( controller='library', action='folder', rename=True, id=folder.id, library_id=library_id )}" method="post" > <div class="form-row"> <label>Name:</label> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/folder_permissions.mako --- a/templates/library/folder_permissions.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/folder_permissions.mako Fri Sep 04 10:31:23 2009 -0400 @@ -15,6 +15,6 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ): +%if trans.app.security_agent.can_manage_library_item( user, roles, folder ): ${render_permission_form( folder, folder.name, h.url_for( controller='library', action='folder', id=folder.id, library_id=library_id, permissions=True ), trans.user.all_roles() )} %endif diff -r adff03258b45 -r 99dcba7af5b6 templates/library/ldda_edit_info.mako --- a/templates/library/ldda_edit_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/ldda_edit_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -34,7 +34,7 @@ </select> </%def> -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): +%if trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ): <div class="toolForm"> <div class="toolFormTitle">Edit attributes of ${ldda.name}</div> <div class="toolFormBody"> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/ldda_info.mako --- a/templates/library/ldda_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/ldda_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -40,15 +40,15 @@ Information about ${ldda.name} <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + %if trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ): <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> %else: <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a> %endif - %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ): + %if trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ) and trans.app.security_agent.can_manage_library_item( user, roles, ldda.library_dataset ): <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> %endif - %if current_version and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + %if current_version and trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ): <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> %endif %if ldda.has_data: @@ -86,28 +86,14 @@ <div class="form-row"> <div>${ldda.blurb}</div> </div> - <div class="form-row"> - <div id="info${ldda.id}" class="historyItemBody"> - %if ldda.peek != "no peek": + %if ldda.peek != "no peek": + <div class="form-row"> + <div id="info${ldda.id}" class="historyItemBody"> <label>Peek:</label> <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div> - %endif - ## Recurse for child datasets - ## TODO: eliminate this - child datasets are deprecated, and where does - ## render_dataset() come from anyway - it's not imported! - %if len( ldda.visible_children ) > 0: - <div> - There are ${len( ldda.visible_children )} secondary datasets. - %for idx, child in enumerate( ldda.visible_children ): - ## TODO: do we need to clarify if the child is deleted? - %if not child.purged: - ${ render_dataset( child, selected, library ) } - %endif - %endfor - </div> - %endif + </div> </div> - </div> + %endif </div> %if widgets: ${render_template_info( ldda, library_id, widgets, editable=False )} diff -r adff03258b45 -r 99dcba7af5b6 templates/library/library_dataset_info.mako --- a/templates/library/library_dataset_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/library_dataset_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -21,7 +21,7 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library_dataset ): +%if trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ): <div class="toolForm"> <div class="toolFormTitle">Edit attributes of ${library_dataset.name}</div> <div class="toolFormBody"> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/library_dataset_permissions.mako --- a/templates/library/library_dataset_permissions.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/library_dataset_permissions.mako Fri Sep 04 10:31:23 2009 -0400 @@ -21,7 +21,7 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, user_roles, trans.app.security_agent.permitted_actions.LIBRARY_manage, library_item=library_dataset ): +%if trans.app.security_agent.can_manage_library_item( user, user_roles, library_dataset ): <% roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all() %> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/library_info.mako --- a/templates/library/library_info.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/library_info.mako Fri Sep 04 10:31:23 2009 -0400 @@ -15,7 +15,7 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): +%if trans.app.security_agent.can_modify_library_item( user, roles, library ): <div class="toolForm"> <div class="toolFormTitle">Change library name and description</div> <div class="toolFormBody"> diff -r adff03258b45 -r 99dcba7af5b6 templates/library/library_permissions.mako --- a/templates/library/library_permissions.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/library/library_permissions.mako Fri Sep 04 10:31:23 2009 -0400 @@ -15,7 +15,7 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, user_roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): +%if trans.app.security_agent.can_manage_library_item( user, user_roles, library ): <% roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all() %> diff -r adff03258b45 -r 99dcba7af5b6 templates/mobile/history/detail.mako --- a/templates/mobile/history/detail.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/mobile/history/detail.mako Fri Sep 04 10:31:23 2009 -0400 @@ -37,7 +37,7 @@ <div class="secondary"> ## Body for history items, extra info and actions, data "peek" <% user, roles = trans.get_user_and_roles() %> - %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ): + %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div>You do not have permission to view this dataset.</div> %elif data_state == "queued": <div>Job is waiting to run</div> diff -r adff03258b45 -r 99dcba7af5b6 templates/mobile/manage_library.mako --- a/templates/mobile/manage_library.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/mobile/manage_library.mako Fri Sep 04 10:31:23 2009 -0400 @@ -9,7 +9,7 @@ ${render_msg( msg, messagetype )} %endif -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): +%if trans.app.security_agent.can_modify_library_item( user, roles, library ): <div class="toolForm"> <div class="toolFormTitle">Change library name and description</div> <div class="toolFormBody"> @@ -55,7 +55,7 @@ </div> </div> %endif -%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): +%if trans.app.security_agent.can_manage_library_item( user, roles, library ): <% roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all() %> diff -r adff03258b45 -r 99dcba7af5b6 templates/root/history_common.mako --- a/templates/root/history_common.mako Fri Sep 04 10:23:37 2009 -0400 +++ b/templates/root/history_common.mako Fri Sep 04 10:31:23 2009 -0400 @@ -8,7 +8,7 @@ data_state = data.state user, roles = trans.get_user_and_roles() %> - %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ): + %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${data.id}"> %else: <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}"> @@ -42,7 +42,7 @@ ## Body for history items, extra info and actions, data "peek" <div id="info${data.id}" class="historyItemBody"> - %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ): + %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div>You do not have permission to view this dataset.</div> %elif data_state == "upload": <div>Dataset is uploading</div>

1 0

[hg] galaxy 2658: Added several options to the Samtools pileup tool
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0cb12b9d9d4d changeset: 2658:0cb12b9d9d4d user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Sep 01 17:01:44 2009 -0400 description: Added several options to the Samtools pileup tool 2 file(s) affected in this change: tools/samtools/sam_pileup.py tools/samtools/sam_pileup.xml diffs (107 lines): diff -r a2d69372d699 -r 0cb12b9d9d4d tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py Tue Sep 01 14:20:49 2009 -0400 +++ b/tools/samtools/sam_pileup.py Tue Sep 01 17:01:44 2009 -0400 @@ -4,15 +4,22 @@ Creates a pileup file from a bam file and a reference. usage: %prog [options] - -i, --input1=i: bam file + -p, --input1=p: bam file -o, --output1=o: Output pileup - -r, --ref=r: Reference file type + -R, --ref=R: Reference file type -n, --ownFile=n: User-supplied fasta reference file -d, --dbkey=d: dbkey of user-supplied file -x, --indexDir=x: Index directory -b, --bamIndex=b: BAM index file + -s, --lastCol=s: Print the mapping quality as the last column + -i, --indels=i: Only output lines containing indels + -M, --mapCap=M: Cap mapping quality + -c, --consensus=c: Call the consensus sequence using MAQ consensu model + -T, --theta=T: Theta paramter (error dependency coefficient) + -N, --hapNum=N: Number of haplotypes in sample + -r, --fraction=r: Expected fraction of differences between a pair of haplotypes + -I, --phredProb=I: Phred probability of an indel in sequencing/prep -usage: %prog input1 output1 ref_type refFile ownFile dbkey index_dir bam_index """ import os, sys, tempfile @@ -49,17 +56,20 @@ tmpf0bambai = '%s.bam.bai' % tmpf0.name tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir) tmpf1fai = '%s.fai' % tmpf1.name + opts = '%s %s -M %s' % (('','-s')[options.lastCol=='yes'], ('','-i')[options.indels=='yes'], options.mapCap) + if options.consensus == 'yes': + opts += ' -c -T %s -N %s -r %s -I %s' % (options.theta, options.hapNum, options.fraction, options.phredProb) cmd1 = None cmd2 = 'cp %s %s; cp %s %s' % (options.input1, tmpf0bam, options.bamIndex, tmpf0bambai) - cmd3 = 'samtools pileup -f %s %s > %s 2> /dev/null' + cmd3 = 'samtools pileup %s -f %s %s > %s 2> /dev/null' if options.ref =='indexed': full_path = "%s.fai" % seq_path if not os.path.exists( full_path ): stop_err( "No sequences are available for '%s', request them by reporting this error." % options.dbkey ) - cmd3 = cmd3 % (seq_path, tmpf0bam, options.output1) + cmd3 = cmd3 % (opts, seq_path, tmpf0bam, options.output1) elif options.ref == 'history': cmd1 = 'cp %s %s; cp %s.fai %s' % (options.ownFile, tmpf1.name, options.ownFile, tmpf1fai) - cmd3 = cmd3 % (tmpf1.name, tmpf0bam, options.output1) + cmd3 = cmd3 % (opts, tmpf1.name, tmpf0bam, options.output1) # index reference if necessary if cmd1: try: diff -r a2d69372d699 -r 0cb12b9d9d4d tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Tue Sep 01 14:20:49 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Tue Sep 01 17:01:44 2009 -0400 @@ -13,6 +13,21 @@ --dbkey=${input1.metadata.dbkey} --indexDir=${GALAXY_DATA_INDEX_DIR} --bamIndex=${input1.metadata.bam_index} + --lastCol=$lastCol + --indels=$indels + --mapCap=$mapCap + --consensus=$c.consensus + #if $c.consensus == "yes": + --theta=$c.theta + --hapNum=$c.hapNum + --fraction=$c.fraction + --phredProb=$c.phredProb + #else: + --theta="None" + --hapNum="None" + --fraction="None" + --phredProb="None" + #end if </command> <inputs> <conditional name="refOrHistory"> @@ -31,6 +46,28 @@ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> </when> </conditional> + <param name="lastCol" type="select" label="Whether or not to print the mapping quality as the last column" help="Makes the output easier to parse, but is space inefficient"> + <option value="no">Do not print the mapping quality as the last column</option> + <option value="yes">Print the mapping quality as the last column</option> + </param> + <param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels"> + <option value="no">Print all lines</option> + <option value="yes">Print only lines containing indels</option> + </param> + <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> + <conditional name="c"> + <param name="consensus" type="select" label="Whether or not to call the consensus sequence using the MAQ consensus model"> + <option value="no">Don't use MAQ consensus model</option> + <option value="yes">Use the MAQ consensus model</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="theta" type="float" value="0.85" label="Theta paramter (error dependency coefficient) in the MAQ consensus calling model" /> + <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> + <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> + <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> + </when> + </conditional> </inputs> <outputs> <data format="tabular" name="output1" />

1 0

[hg] galaxy 2657: More performance improvements in checking secu...
by Greg Von Kuster 09 Sep '09

09 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a2d69372d699 changeset: 2657:a2d69372d699 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Sep 01 14:20:49 2009 -0400 description: More performance improvements in checking security on library folders from the Data Libraries view. Fix a bug in the Data Libraries view where empty folders were rendered when they contained no accessible datasets. Clean up requests code that determined the libraries that should be rendered in the select list on the request form. 6 file(s) affected in this change: lib/galaxy/security/__init__.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/library/browse_libraries.mako templates/library/browse_library.mako diffs (521 lines): diff -r d7a780065c91 -r a2d69372d699 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Sat Aug 29 12:08:35 2009 -0400 +++ b/lib/galaxy/security/__init__.py Tue Sep 01 14:20:49 2009 -0400 @@ -101,7 +101,7 @@ if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in dataset.actions ]: # anons only get access, and only if there are no roles required for the access action # Other actions (or if the dataset has roles defined for the access action) fall through - # to the false below + # to the false below for anons return True elif action.action not in [ dp.action for dp in dataset.actions ]: if action.model == 'restrict': @@ -119,28 +119,34 @@ # The user is missing at least one required role return False def allow_library_item_action( self, user, roles, action, library_item ): + """ + Method for checking a permission for the current user to perform a + specific library action on a library item, which must be one of: + Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation + """ if user is None: # All permissions are granted, so non-users cannot have permissions return False - if action.model == 'grant': - # Check to see if user has access to any of the roles - allowed_role_assocs = [] - for item_class, permission_class in self.library_item_assocs: - if isinstance( library_item, item_class ): - if permission_class == self.model.LibraryPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_id=library_item.id ).all() - elif permission_class == self.model.LibraryFolderPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_folder_id=library_item.id ).all() - elif permission_class == self.model.LibraryDatasetPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_dataset_id=library_item.id ).all() - elif permission_class == self.model.LibraryDatasetDatasetAssociationPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_dataset_dataset_association_id=library_item.id ).all() - for allowed_role_assoc in allowed_role_assocs: - if allowed_role_assoc.role in roles: - return True - return False - else: - raise 'Unimplemented model (%s) specified for action (%s)' % ( action.model, action.action ) + # Check to see if user has access to any of the roles + allowed_role_assocs = [] + for item_class, permission_class in self.library_item_assocs: + if isinstance( library_item, item_class ): + if permission_class == self.model.LibraryPermissions: + allowed_role_assocs = permission_class.filter_by( action=action.action, + library=library_item ).all() + elif permission_class == self.model.LibraryFolderPermissions: + allowed_role_assocs = permission_class.filter_by( action=action.action, + folder=library_item ).all() + elif permission_class == self.model.LibraryDatasetPermissions: + allowed_role_assocs = permission_class.filter_by( action=action.action, + library_dataset=library_item ).all() + elif permission_class == self.model.LibraryDatasetDatasetAssociationPermissions: + allowed_role_assocs = permission_class.filter_by( action=action.action, + library_dataset_dataset_association=library_item ).all() + for allowed_role_assoc in allowed_role_assocs: + if allowed_role_assoc.role in roles: + return True + return False def get_item_action( self, action, item ): # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation for permission in item.actions: @@ -291,7 +297,10 @@ permissions[ action ] = [ dhp.role ] return permissions def set_all_dataset_permissions( self, dataset, permissions={} ): - # Set new permissions on a dataset, eliminating all current permissions + """ + Set new permissions on a dataset, eliminating all current permissions + permissions looks like: { Action : [ Role, Role ] } + """ # Delete all of the current permissions on the dataset # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, # or the dataset is inaccessible. See admin/library_dataset_dataset_association() @@ -305,7 +314,10 @@ for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: dp.flush() def set_dataset_permission( self, dataset, permission={} ): - # Set a specific permission on a dataset, leaving all other current permissions on the dataset alone + """ + Set a specific permission on a dataset, leaving all other current permissions on the dataset alone + permissions looks like: { Action : [ Role, Role ] } + """ # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, # or the dataset is inaccessible. See admin/library_dataset_dataset_association() for action, roles in permission.items(): @@ -331,8 +343,11 @@ dp.delete() dp.flush() def get_dataset_permissions( self, dataset ): - if not isinstance( dataset, self.model.Dataset ): - dataset = dataset.dataset + """ + Return a dictionary containing the actions and associated roles on dataset. + The dictionary looks like: { Action : [ Role, Role ] } + dataset must be an instance of Dataset() + """ permissions = {} for dp in dataset.actions: action = self.get_action( dp.action ) @@ -423,18 +438,29 @@ else: raise 'Invalid class (%s) specified for target_library_item (%s)' % \ ( target_library_item.__class__, target_library_item.__class__.__name__ ) - def show_library_item( self, user, roles, library_item ): - if self.allow_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, library_item=library_item ) or \ - self.allow_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, library_item=library_item ) or \ - self.allow_action( user, roles, self.permitted_actions.LIBRARY_ADD, library_item=library_item ): - return True + def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): + """ + This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with + the string, True is returned if the current user has permission to perform any 1 of actions_to_check + on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets + this criteria, if it exists. + """ + for action in actions_to_check: + if self.allow_library_item_action( user, roles, action, library_item ): + return True, hidden_folder_ids if isinstance( library_item, self.model.Library ): - return self.show_library_item( user, roles, library_item.root_folder ) - elif isinstance( library_item, self.model.LibraryFolder ): - for folder in library_item.folders: - if self.show_library_item( user, roles, folder ): - return True - return False + return self.show_library_item( user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) + if isinstance( library_item, self.model.LibraryFolder ): + for folder in library_item.active_folders: + can_show, hidden_folder_ids = self.show_library_item( user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) + if can_show: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, folder.id ) + else: + hidden_folder_ids = '%d' % folder.id + return False, hidden_folder_ids def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): for user in users: if delete_existing_assocs: @@ -482,10 +508,12 @@ if 'role' in kwd: return self.model.GroupRoleAssociation.filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first() raise 'No valid method of associating provided components: %s' % kwd - def check_folder_contents( self, user, roles, folder ): + def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ): """ - Return true if there are any datasets under 'folder' that are public or that the - user has access permission on. + This method must always be sent an instance of LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along + with the string, True is returned if the current user has permission to access folder. Otherwise, + cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. """ action = self.permitted_actions.DATASET_ACCESS.action lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ @@ -498,14 +526,19 @@ ldda_access = self.get_item_action( action, ldda.dataset ) if ldda_access is None: # Dataset is public - return True + return True, hidden_folder_ids if ldda_access.role in roles: # The current user has access permission on the dataset - return True + return True, hidden_folder_ids for sub_folder in folder.active_folders: - if self.check_folder_contents( user, roles, sub_folder ): - return True - return False + can_access, hidden_folder_ids = self.check_folder_contents( user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids ) + if can_access: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, sub_folder.id ) + else: + hidden_folder_ids = '%d' % sub_folder.id + return False, hidden_folder_ids class HostAgent( RBACAgent ): """ diff -r d7a780065c91 -r a2d69372d699 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Sat Aug 29 12:08:35 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue Sep 01 14:20:49 2009 -0400 @@ -65,23 +65,24 @@ user, roles = trans.get_user_and_roles() all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \ .order_by( trans.app.model.Library.name ).all() - authorized_libraries = [] + library_actions = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD, + trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, + trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] + # The authorized_libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the browse_library() method and the browse_library.mako template to keep from re-checking the + # same folders when the library is rendered. + authorized_libraries = {} for library in all_libraries: - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_ADD, - library_item=library ) or \ - trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=library ) or \ - trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, - library_item=library ) or \ - trans.app.security_agent.check_folder_contents( user, roles, library.root_folder ) or \ - trans.app.security_agent.show_library_item( user, roles, library ): - authorized_libraries.append( library ) + can_access, hidden_folder_ids = trans.app.security_agent.check_folder_contents( user, roles, library.root_folder ) + if can_access: + authorized_libraries[ library ] = hidden_folder_ids + else: + can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, library_actions ) + if can_show: + authorized_libraries[ library ] = hidden_folder_ids return trans.fill_template( '/library/browse_libraries.mako', libraries=authorized_libraries, default_action=params.get( 'default_action', None ), @@ -94,6 +95,7 @@ messagetype = params.get( 'messagetype', 'done' ) id = params.get( 'id', None ) if not id: + # To handle bots msg = "You must specify a library id." return trans.response.send_redirect( web.url_for( controller='library', action='browse_libraries', @@ -102,6 +104,7 @@ messagetype='error' ) ) library = library=trans.app.model.Library.get( id ) if not library: + # To handle bots msg = "Invalid library id ( %s )." return trans.response.send_redirect( web.url_for( controller='library', action='browse_libraries', @@ -109,9 +112,11 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) + hidden_folder_ids = util.listify( util.restore_text( params.get( 'hidden_folder_ids', '' ) ) ) return trans.fill_template( '/library/browse_library.mako', library=trans.app.model.Library.get( id ), created_ldda_ids=created_ldda_ids, + hidden_folder_ids=hidden_folder_ids, default_action=params.get( 'default_action', None ), comptypes=comptypes, msg=msg, @@ -1197,25 +1202,3 @@ edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) - -def get_authorized_libs( trans, user ): - # TODO: this is a mis-named function - the name should reflect the authorization policy - # If user is not authenticated, this method should not even be called. Also, it looks - # like all that is using this is the new request stuff, so it should be placed there. - if not user: - return [] - roles = user.all_roles() - all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ - .order_by( trans.app.model.Library.name ).all() - authorized_libraries = [] - for library in all_libraries: - if trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_ADD, - library_item=library ) \ - or trans.app.security_agent.allow_action( user, - roles, - trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, - library_item=library ): - authorized_libraries.append( library ) - return authorized_libraries diff -r d7a780065c91 -r a2d69372d699 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sat Aug 29 12:08:35 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Tue Sep 01 14:20:49 2009 -0400 @@ -9,8 +9,6 @@ from datetime import datetime, timedelta from cgi import escape, FieldStorage from galaxy.web.controllers.forms import get_form_widgets -from galaxy.web.controllers.library import get_authorized_libs - log = logging.getLogger( __name__ ) @@ -432,8 +430,6 @@ return self.__show_request_form(trans, **kwd) elif params.get('refresh', False) == 'true': return self.__show_request_form(trans, **kwd) - - def __show_request_form(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -460,7 +456,25 @@ helptext='(Optional)')) # libraries selectbox - libraries = get_authorized_libs(trans, trans.user) + all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ).all() + user, roles = trans.get_user_and_roles() + actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] + # The libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + # + # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids + # so that you do not need to check those same folders yet again when populating the select list. + # + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids libui = self.__library_ui(libraries, **kwd) widgets = widgets + libui widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], **kwd) @@ -470,12 +484,10 @@ widgets=widgets, msg=msg, messagetype=messagetype) - def __library_ui(self, libraries, request=None, **kwd): params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - lib_list = SelectField('library_id', refresh_on_change=True, - refresh_on_change_values=['new']) + lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=['new'] ) if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) @@ -483,7 +495,7 @@ lib_list.add_option('Select one', 'none', selected=True) else: lib_list.add_option('Select one', 'none') - for lib in libraries: + for lib, hidden_folder_ids in libraries.items(): if str(lib.id) == lib_id: lib_list.add_option(lib.name, lib.id, selected=True) else: @@ -653,9 +665,27 @@ widgets.append(dict(label='Description', widget=TextField('desc', 40, desc), helptext='(Optional)')) - # libraries selectbox - libraries = get_authorized_libs(trans, trans.user) + all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ).all() + user, roles = trans.get_user_and_roles() + actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] + # The libraries dictionary looks like: + # { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + # + # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids + # so that you do not need to check those same folders yet again when populating the select list. + # + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids libui = self.__library_ui(libraries, request, **kwd) widgets = widgets + libui widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, **kwd) diff -r d7a780065c91 -r a2d69372d699 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sat Aug 29 12:08:35 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Sep 01 14:20:49 2009 -0400 @@ -8,7 +8,6 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from galaxy.web.controllers.forms import get_form_widgets -from galaxy.web.controllers.library import get_authorized_libs log = logging.getLogger( __name__ ) @@ -709,14 +708,32 @@ return select_user def __library_ui(self, trans, user, request=None, **kwd): + """ + Return a list of libraries for which user has the permission + to perform the LIBRARY_ADD action on any of it's folders + """ params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - if not user: - libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() - else: - libraries = get_authorized_libs(trans, user) - lib_list = SelectField('library_id', refresh_on_change=True, - refresh_on_change_values=['new']) + all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ).all() + roles = user.all_roles() + actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] + # The libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + # + # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids + # so that you do not need to check those same folders yet again when populating the select list. + # + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids + lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=['new'] ) if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) @@ -724,7 +741,7 @@ lib_list.add_option('Select one', 'none', selected=True) else: lib_list.add_option('Select one', 'none') - for lib in libraries: + for lib, hidden_folder_ids in libraries.items(): if str(lib.id) == lib_id: lib_list.add_option(lib.name, lib.id, selected=True) else: diff -r d7a780065c91 -r a2d69372d699 templates/library/browse_libraries.mako --- a/templates/library/browse_libraries.mako Sat Aug 29 12:08:35 2009 -0400 +++ b/templates/library/browse_libraries.mako Tue Sep 01 14:20:49 2009 -0400 @@ -20,9 +20,9 @@ </tr> </thead> <tbody> - %for library in libraries: + %for library, hidden_folder_ids in libraries.items(): <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><a href="${h.url_for( controller='library', action='browse_library', id=library.id )}">${library.name}</a></td> + <td><a href="${h.url_for( controller='library', action='browse_library', id=library.id, hidden_folder_ids=hidden_folder_ids )}">${library.name}</a></td> <td><i>${library.description}</i></td> </tr> %endfor diff -r d7a780065c91 -r a2d69372d699 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Sat Aug 29 12:08:35 2009 -0400 +++ b/templates/library/browse_library.mako Tue Sep 01 14:20:49 2009 -0400 @@ -3,7 +3,6 @@ <% from galaxy import util from time import strftime - user, roles = trans.get_user_and_roles() %> @@ -142,19 +141,21 @@ %> </%def> -<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, parent=None, row_counter=None )"> +<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None )"> <% - def show_folder(): - ## TODO: instead of calling check_folder_contents(), which we've already done prior to getting here, - ## add a new method that will itself call check_folder_contents() and build a list of accessible folders - ## for each library - this should improve performance dor large libraries where the current user can only - ## access a small number of folders. - if trans.app.security_agent.check_folder_contents( user, roles, folder ) or \ - trans.app.security_agent.show_library_item( user, roles, folder ): - return True - return False - if not show_folder: + if str( folder.id ) in hidden_folder_ids: return "" + can_access, folder_ids = trans.app.security_agent.check_folder_contents( user, roles, folder ) + if not can_access: + can_show, folder_ids = \ + trans.app.security_agent.show_library_item( user, + roles, + folder, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD, + trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, + trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] ) + if not can_show: + return "" root_folder = not folder.parent if root_folder: pad = folder_pad @@ -213,7 +214,7 @@ %> %endif %for child_folder in name_sorted( folder.active_folders ): - ${render_folder( child_folder, pad, created_ldda_ids, library_id, my_row, row_counter )} + ${render_folder( child_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, my_row, row_counter )} %endfor %for library_dataset in name_sorted( folder.active_library_datasets ): <% @@ -272,7 +273,7 @@ </thead> </tr> <% row_counter = RowCounter() %> - ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, None, row_counter )} + ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, hidden_folder_ids, None, row_counter )} <tfoot> <tr> <td colspan="4" style="padding-left: 42px;">

1 0

Managed releases?
by Chris Cole 09 Sep '09

09 Sep '09

Hi, I have a local install of Galaxy and would like to keep up-to-date with the latest updates, but I'm not sure what functionality has changed nor how significant the changes are. The mercurial updates on this list are too detailed. I just want to know what the benefit of an update would be, not which files have changed. Would it be possible to start having more managed releases with a changelog between each release? That way it will be much clearer what the functional benefits of updating to a newer release would be. Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

4 6

library upload docs
by Kimberly Begley 09 Sep '09

09 Sep '09

Hello, Where can I find documentation on how to upload a library dataset and assign roles to users and groups for a local Galaxy installation? Thanks, Kimberly

2 1