galaxy-commits February 2011

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commit/galaxy-central: jgoecks: Fix searching functionality and labels in published item grids.
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a8bfcfeca73b/ changeset: r5045:a8bfcfeca73b user: jgoecks date: 2011-02-11 14:42:05 summary: Fix searching functionality and labels in published item grids. affected #: 4 files (174 bytes) --- a/lib/galaxy/web/controllers/history.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/history.py Fri Feb 11 08:42:05 2011 -0500 @@ -135,15 +135,15 @@ columns = [ NameURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] --- a/lib/galaxy/web/controllers/page.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/page.py Fri Feb 11 08:42:05 2011 -0500 @@ -63,15 +63,15 @@ columns = [ grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], + "Search title, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, trans, **kwargs ): --- a/lib/galaxy/web/controllers/visualization.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Fri Feb 11 08:42:05 2011 -0500 @@ -50,15 +50,15 @@ columns = [ grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ], + "Search title, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, trans, **kwargs ): --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 11 00:53:49 2011 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Fri Feb 11 08:42:05 2011 -0500 @@ -66,15 +66,15 @@ columns = [ grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available
by Bitbucket 11 Feb '11

11 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/384f3b803e64/ changeset: r5044:384f3b803e64 user: kanwei date: 2011-02-11 06:53:49 summary: trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available affected #: 3 files (329 bytes) --- a/lib/galaxy/datatypes/interval.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/datatypes/interval.py Fri Feb 11 00:53:49 2011 -0500 @@ -1161,7 +1161,7 @@ resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack", {"data": "bigwig"} + return "LineTrack", {"data": "bigwig", "index": "bigwig"} class CustomTrack ( Tabular ): """UCSC CustomTrack""" --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri Feb 11 00:53:49 2011 -0500 @@ -48,13 +48,13 @@ # Override. pass - def has_data( self, chrom, start, end ): + def has_data( self, chrom, start, end, **kwargs ): """ Returns true if dataset has data in the specified genome window, false otherwise. """ # Override. - return False + pass def get_data( self, chrom, start, end, **kwargs ): """ Returns data in region defined by chrom, start, and end. """ @@ -140,10 +140,9 @@ else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] - def has_data( self, chrom, start, end ): + def has_data( self, chrom ): """ - Returns true if dataset has data in the specified genome window, false - otherwise. + Returns true if dataset has data for this chrom """ # Get summary tree. @@ -154,8 +153,7 @@ self.CACHE[filename] = st # Check for data. - level = ceil( log( 100000, st.block_size ) ) - 1 - return ( st.query( chrom, int(start), int(end), level ) is not None ) + return st.chrom_blocks.get(chrom, None) is not None class VcfDataProvider( TracksDataProvider ): """ @@ -405,14 +403,24 @@ """ BigWig data provider for the Galaxy track browser. """ - - def get_data( self, chrom, start, end, **kwargs ): - # Bigwig has the possibility of it being a standalone bigwig file, in which case we use - # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + def _get_dataset( self ): if self.converted_dataset is not None: f = open( self.converted_dataset.file_name ) else: f = open( self.original_dataset.file_name ) + return f + + def has_data( self, chrom ): + f = self._get_dataset() + bw = BigWigFile(file=f) + all_dat = bw.query(chrom, 0, 2147483647, 1) + f.close() + return all_dat is not None + + def get_data( self, chrom, start, end, **kwargs ): + # Bigwig has the possibility of it being a standalone bigwig file, in which case we use + # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + f = self._get_dataset() bw = BigWigFile(file=f) if 'stats' in kwargs: @@ -426,7 +434,6 @@ 'min': float( all_dat['min'] ), \ 'total_frequency': float( all_dat['coverage'] ) } - start = int(start) end = int(end) num_points = 2000 @@ -439,9 +446,10 @@ pos = start step_size = (end - start) / num_points result = [] - for dat_dict in data: - result.append( (pos, float_nan(dat_dict['mean']) ) ) - pos += step_size + if data: + for dat_dict in data: + result.append( (pos, float_nan(dat_dict['mean']) ) ) + pos += step_size return result --- a/lib/galaxy/web/controllers/tracks.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 11 00:53:49 2011 -0500 @@ -458,13 +458,17 @@ return msg # Check for data in the genome window. - # TODO: Not all tracks have an index data source, so need to try alternative data sources to check for data. - if chrom and low and high and data_sources.get( 'index' ): + if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) - if not indexer.has_data( chrom, low, high ): + if not indexer.has_data( chrom ): return messages.NO_DATA - + else: + # Standalone data provider + standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) + kwargs = {"stats": True} + if not standalone_provider.has_data( chrom ): + return messages.NO_DATA return messages.DATA @web.json Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: trackster: Remove content-div margin and border-top
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7234805d1f92/ changeset: r5043:7234805d1f92 user: kanwei date: 2011-02-10 23:43:39 summary: trackster: Remove content-div margin and border-top affected #: 2 files (63 bytes) --- a/static/june_2007_style/blue/trackster.css Thu Feb 10 17:19:40 2011 -0500 +++ b/static/june_2007_style/blue/trackster.css Thu Feb 10 17:43:39 2011 -0500 @@ -22,7 +22,7 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{overflow:hidden;text-align:center;margin-bottom:2px;border-top:1px solid #eee;border-bottom:#eee solid 1px;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{overflow:hidden;text-align:center;border-bottom:1px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} --- a/static/june_2007_style/trackster.css.tmpl Thu Feb 10 17:19:40 2011 -0500 +++ b/static/june_2007_style/trackster.css.tmpl Thu Feb 10 17:43:39 2011 -0500 @@ -146,9 +146,8 @@ .track-content { overflow: hidden; text-align: center; - margin-bottom: 2px; - border-top: 1px solid #eee; - border-bottom: #eee solid 1px; +/* border-top: 1px solid #eee; */ + border-bottom: 1px solid #eee; background: #eee url('/static/images/tracks/diag_bg.gif'); min-height: 16px; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c2d187cf4428/ changeset: r5042:c2d187cf4428 user: jgoecks date: 2011-02-10 23:19:40 summary: Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality. affected #: 5 files (5.5 KB) --- a/lib/galaxy/datatypes/util/gff_util.py Thu Feb 10 15:53:06 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Thu Feb 10 17:19:40 2011 -0500 @@ -257,4 +257,18 @@ # Could not split attributes string, so entire string must be # 'group' attribute. This is the case for strictly GFF files. attributes['group'] = attr_str - return attributes \ No newline at end of file + return attributes + +def gff_attributes_to_str( attrs, gff_format ): + """ + Convert GFF attributes to string. Supported formats are GFF3, GTF. + """ + if gff_format == 'GTF': + format_string = '%s "%s"' + elif gff_format == 'GFF3': + format_string = '%s=%s' + attrs_strs = [] + for name, value in attrs.items(): + attrs_strs.append( format_string % ( name, value ) ) + return " ; ".join( attrs_strs ) + \ No newline at end of file --- a/tools/extract/extract_genomic_dna.py Thu Feb 10 15:53:06 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Thu Feb 10 17:19:40 2011 -0500 @@ -5,17 +5,19 @@ -d, --dbkey=N: Genome build of input file -o, --output_format=N: the data type of the output file -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc + -I, --interpret_features: if true, complete features are interpreted when input is GFF + -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format. """ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) -import sys, string, os, re +import sys, string, os, re, tempfile, subprocess from bx.cookbook import doc_optparse import bx.seq.nib import bx.seq.twobit from galaxy.tools.util.galaxyops import * -from galaxy.datatypes.util.gff_util import * +from galaxy.datatypes.util import gff_util assert sys.version_info[:2] >= ( 2, 4 ) @@ -44,16 +46,20 @@ seq_path = fields[2].strip() break return seq_path - def __main__(): + # + # Parse options, args. + # options, args = doc_optparse.parse( __doc__ ) try: chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols ) dbkey = options.dbkey output_format = options.output_format gff_format = options.gff + interpret_features = options.interpret_features GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR + fasta_file = options.fasta input_filename, output_filename = args except: doc_optparse.exception() @@ -62,11 +68,49 @@ strand = None nibs = {} twobits = {} - seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) - if not os.path.exists( seq_path ): - # If this occurs, we need to fix the metadata validator. - stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey ) + + # + # Set path to sequence data. + # + if fasta_file: + # Need to create 2bit file from fasta file. + try: + seq_path = tempfile.NamedTemporaryFile( dir="." ).name + cmd = "faToTwoBit %s %s" % ( fasta_file, seq_path ) + + tmp_name = tempfile.NamedTemporaryFile( dir="." ).name + tmp_stderr = open( tmp_name, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # Get stderr, allowing for case where it's very large. + tmp_stderr = open( tmp_name, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + + # Error checking. + if returncode != 0: + raise Exception, stderr + except Exception, e: + stop_err( 'Error running faToTwoBit. ' + str( e ) ) + else: + seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) + if not os.path.exists( seq_path ): + # If this occurs, we need to fix the metadata validator. + stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey ) + + # + # Fetch sequences. + # skipped_lines = 0 first_invalid_line = 0 invalid_line = '' @@ -74,106 +118,134 @@ warnings = [] warning = '' twobitfile = None - - for i, line in enumerate( open( input_filename ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + file_iterator = open( input_filename ) + if gff_format and interpret_features: + file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=True ) + for i, feature in enumerate( file_iterator ): + if gff_format and interpret_features: + # Processing features. + gff_util.convert_gff_coords_to_bed( feature ) + chrom = feature.chrom + start = feature.start + end = feature.end + strand = feature.strand + else: + # Processing lines, either interval or GFF format. + line = feature.rstrip( '\r\n' ) + if line and not line.startswith( "#" ): + fields = line.split( '\t' ) + try: + chrom = fields[chrom_col] + start = int( fields[start_col] ) + end = int( fields[end_col] ) + if gff_format: + start, end = gff_util.convert_gff_coords_to_bed( [start, end] ) + if includes_strand_col: + strand = fields[strand_col] + except: + warning = "Invalid chrom, start or end column values. " + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if start > end: + warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + + if strand not in ['+', '-']: + strand = '+' + sequence = '' + + # Open sequence file and get sequence for feature/interval. + if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): + # TODO: improve support for GFF-nib interaction. + if chrom in nibs: + nib = nibs[chrom] + else: + nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: - chrom = fields[chrom_col] - start = int( fields[start_col] ) - end = int( fields[end_col] ) - if gff_format: - start, end = convert_gff_coords_to_bed( [start, end] ) - if includes_strand_col: - strand = fields[strand_col] + sequence = nib.get( start, end-start ) except: - warning = "Invalid chrom, start or end column values. " + warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) warnings.append( warning ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 invalid_line = line continue - if start > end: - warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end ) + elif seq_path and os.path.isfile( seq_path ): + if not(twobitfile): + twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) ) + try: + if options.gff and interpret_features: + # Create sequence from intervals within a feature. + sequence = '' + for interval in feature.intervals: + sequence += twobitfile[interval.chrom][interval.start:interval.end] + else: + sequence = twobitfile[chrom][start:end] + except: + warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) warnings.append( warning ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 invalid_line = line continue + else: + warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if sequence == '': + warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \ + % ( chrom, start, end, dbkey ) + warnings.append( warning ) + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + if includes_strand_col and strand == "-": + sequence = reverse_complement( sequence ) - if strand not in ['+', '-']: - strand = '+' - sequence = '' - - if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): - if chrom in nibs: - nib = nibs[chrom] - else: - nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) - try: - sequence = nib.get( start, end-start ) - except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - elif seq_path and os.path.isfile( seq_path ): - if not(twobitfile): - twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) ) - try: - sequence = twobitfile[chrom][start:end] - except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue + if output_format == "fasta" : + l = len( sequence ) + c = 0 + if gff_format: + start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] ) + fields = [dbkey, str( chrom ), str( start ), str( end ), strand] + meta_data = "_".join( fields ) + fout.write( ">%s\n" % meta_data ) + while c < l: + b = min( c + 50, l ) + fout.write( "%s\n" % str( sequence[c:b] ) ) + c = b + else: # output_format == "interval" + if interpret_features: + # TODO: need better GFF Reader to capture all information needed + # to produce this line. + meta_data = "\t".join( + [feature.chrom, "galaxy_extract_genomic_dna", "interval", \ + str( feature.start ), str( feature.end ), feature.score, feature.strand, + ".", gff_util.gff_attributes_to_str( feature.attributes, "GTF" ) ] ) else: - warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - if sequence == '': - warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " %( chrom, start, end, dbkey ) - warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line - continue - if includes_strand_col and strand == "-": - sequence = reverse_complement( sequence ) - - if output_format == "fasta" : - l = len( sequence ) - c = 0 - if gff_format: - start, end = convert_bed_coords_to_gff( [ start, end ] ) - fields = [dbkey, str( chrom ), str( start ), str( end ), strand] - meta_data = "_".join( fields ) - fout.write( ">%s\n" % meta_data ) - while c < l: - b = min( c + 50, l ) - fout.write( "%s\n" % str( sequence[c:b] ) ) - c = b - else: # output_format == "interval" meta_data = "\t".join( fields ) - if gff_format: - format_str = "%s seq \"%s\";\n" - else: - format_str = "%s\t%s\n" - fout.write( format_str % ( meta_data, str( sequence ) ) ) + if gff_format: + format_str = "%s seq \"%s\";\n" + else: + format_str = "%s\t%s\n" + fout.write( format_str % ( meta_data, str( sequence ) ) ) fout.close() --- a/tools/extract/extract_genomic_dna.xml Thu Feb 10 15:53:06 2011 -0500 +++ b/tools/extract/extract_genomic_dna.xml Thu Feb 10 17:19:40 2011 -0500 @@ -1,57 +1,112 @@ <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python"> - extract_genomic_dna.py $input $out_file1 -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR} + extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey + + #if str( $interpret_features ) == "yes": + -I + #end if + + ## Columns to use in input file. #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): -1 1,4,5,7 --gff #else: -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} #end if + + #if $seq_source.index_source == "cached": + ## Genomic data from cache. + -g ${GALAXY_DATA_INDEX_DIR} + #else: + ## Genomic data from history. + -F $seq_source.ref_file + #end if </command><inputs> - <param format="interval,gff" name="input" type="data" label="Fetch sequences corresponding to Query"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" /> - </param> - <param name="out_format" type="select" label="Output data type"> - <option value="fasta">FASTA</option> - <option value="interval">Interval</option> - </param> + <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"> + <validator type="unspecified_build" /> + </param> + <param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for Genomic Data"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="out_format" type="select" label="Output data type"> + <option value="fasta">FASTA</option> + <option value="interval">Interval</option> + </param></inputs><outputs> - <data format="input" name="out_file1" metadata_source="input"> - <change_format> - <when input="out_format" value="fasta" format="fasta" /> - </change_format> - </data> + <data format="input" name="out_file1" metadata_source="input"> + <change_format> + <when input="out_format" value="fasta" format="fasta" /> + </change_format> + </data></outputs><tests><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="cached"/><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out1.fasta" /></test><test><param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="cached"/><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out2.fasta" /></test><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" /></test><test><param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out4.gff" /></test><test><param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/><param name="out_format" value="fasta"/> + <param name="index_source" value="cached"/><output name="out_file1" file="extract_genomic_dna_out5.fasta" /></test> +  + <test> + <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="no"/> + <param name="index_source" value="history"/> + <param name="ref_file" value="tophat_in1.fasta"/> + <param name="out_format" value="fasta"/> + <output name="out_file1" file="extract_genomic_dna_out6.fasta" /> + </test> + <test> + <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> + <param name="interpret_features" value="yes"/> + <param name="index_source" value="history"/> + <param name="ref_file" value="tophat_in1.fasta"/> + <param name="out_format" value="fasta"/> + <output name="out_file1" file="extract_genomic_dna_out7.fasta" /> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Another bugfix for egg conflicts, don't add items to the pkg_resources working set unless the item's not already in there.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6d5331f3b468/ changeset: r5041:6d5331f3b468 user: natefoo date: 2011-02-10 21:53:06 summary: Another bugfix for egg conflicts, don't add items to the pkg_resources working set unless the item's not already in there. affected #: 1 file (79 bytes) --- a/lib/galaxy/eggs/__init__.py Thu Feb 10 15:29:08 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Thu Feb 10 15:53:06 2011 -0500 @@ -212,7 +212,8 @@ try: dists = self.resolve() for dist in dists: - pkg_resources.working_set.add( dist ) + if dist.location not in pkg_resources.working_set.entries: + pkg_resources.working_set.add( dist ) return dists except: raise Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Migration script to add a subindex column to the run table.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b8442c5e90c9/ changeset: r5040:b8442c5e90c9 user: greg date: 2011-02-10 21:29:08 summary: Migration script to add a subindex column to the run table. affected #: 3 files (108 bytes) --- a/lib/galaxy/model/__init__.py Thu Feb 10 13:58:48 2011 -0500 +++ b/lib/galaxy/model/__init__.py Thu Feb 10 15:29:08 2011 -0500 @@ -2050,9 +2050,10 @@ self.external_service = external_service class Run( object ): - def __init__( self, form_definition, form_values ): + def __init__( self, form_definition, form_values, subindex=None ): self.template = form_definition self.info = form_values + self.subindex = subindex class RequestTypeRunAssociation( object ): def __init__( self, request_type, run ): --- a/lib/galaxy/model/mapping.py Thu Feb 10 13:58:48 2011 -0500 +++ b/lib/galaxy/model/mapping.py Thu Feb 10 15:29:08 2011 -0500 @@ -705,7 +705,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "subindex", TrimmedString( 255 ), index=True ) ) RequestTypeRunAssociation.table = Table( "request_type_run_association", metadata, Column( "id", Integer, primary_key=True ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: workflows: jquery1.5 fix, quotations.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9b43e6baee92/ changeset: r5039:9b43e6baee92 user: dannon date: 2011-02-10 19:58:48 summary: workflows: jquery1.5 fix, quotations. affected #: 2 files (4 bytes) --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Feb 10 12:13:55 2011 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Feb 10 13:58:48 2011 -0500 @@ -409,7 +409,7 @@ var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); // If already connected save old connection - old_body.find( "div[name=" + input.name + "]" ).each( function() { + old_body.find( "div[name='" + input.name + "']" ).each( function() { $(this).find( ".input-terminal" ).each( function() { var c = this.terminal.connectors[0]; if ( c ) { --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Feb 10 12:13:55 2011 -0500 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Feb 10 13:58:48 2011 -0500 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var 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b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix for pysam egg conditional, which would always fail, and actually check always_conditional eggs in the crate's all_eggs method. Fixes downloading of eggs for offline systems.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/559a9ad2844d/ changeset: r5038:559a9ad2844d user: natefoo date: 2011-02-10 18:13:55 summary: Fix for pysam egg conditional, which would always fail, and actually check always_conditional eggs in the crate's all_eggs method. Fixes downloading of eggs for offline systems. affected #: 1 file (82 bytes) --- a/lib/galaxy/eggs/__init__.py Thu Feb 10 10:33:08 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Thu Feb 10 12:13:55 2011 -0500 @@ -295,8 +295,9 @@ """ rval = [] for egg in self.eggs.values(): - if egg.name not in self.galaxy_config.always_conditional: - rval.append( egg ) + if egg.name in self.galaxy_config.always_conditional and not self.galaxy_config.check_conditional( egg.name ): + continue + rval.append( egg ) return rval def __getitem__( self, name ): """ @@ -357,7 +358,7 @@ "python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ), "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "ctypes": lambda: ( "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(",") ) and sys.version_info[:2] == ( 2, 4 ), - "pysam": check_pysam() + "pysam": lambda: check_pysam() }.get( egg_name, lambda: True )() except: return False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d5ce1d53e611/ changeset: r5037:d5ce1d53e611 user: guru date: 2011-02-10 16:33:08 summary: Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool. affected #: 2 files (2.6 KB) --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Thu Feb 10 10:33:08 2011 -0500 @@ -18,7 +18,12 @@ #------------------------------------------------------------------------------- # WHICH SPUTNIK USED? my $sputnikpath = (); -$sputnikpath = "sputnik" ; +$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC"; +#print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath; +#exit if !-e $sputnikpath; +#$sputnikpath = "bx-sputnik" ; +#print "ARGV input = @ARGV\n"; +#print "ARGV input :\n mafile=$mafile\n orthfile=$orthfile\n threshold_array=$threshold_array\n species_set=$species_set\n tree_definition=$tree_definition\n separation=$separation\n"; #------------------------------------------------------------------------------- # RUNFILE #------------------------------------------------------------------------------- @@ -37,9 +42,12 @@ my $tdir = tempdir( CLEANUP => 0 ); chdir $tdir; my $dir = getcwd; +#print "current dit=$dir\n"; #------------------------------------------------------------------------------- # CREATE AXT FILES IN FORWARD AND REVERSE ORDERS IF NECESSARY my @chrfiles=(); + +#my $mafile = "/Users/ydk/work/rhesus_microsat/results/galay/align.txt"; #$ARGV[0]; my $chromt=int(rand(10000)); my $p_chr=$chromt; @@ -54,20 +62,27 @@ push @exactspecies, $spec if $spec eq $espec; } } +#print "exactspecies=@exactspecies\n"; my $focalspec = $exactspecies[0]; my $arranged_species_set=join(".",@exactspecies); my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt"); +#print "sending to maftoAxt_multispecies: $mafile, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; maftoAxt_multispecies($mafile, $tree_definition, $chr_name, $species_set); +#print "done maf to axt conversion\n"; my $reverse_chr_name = join(".",("chr".$p_chr."r"),$arranged_species_set, "net", "axt"); artificial_axdata_inverter ($chr_name, $reverse_chr_name); +#print "reverse_chr_name=$reverse_chr_name\n"; #------------------------------------------------------------------------------- +# FIND THE CORRESPONDING CHIMP CHROMOSOME FROM FILE ORTp_chrS.TXT foreach my $direct ("reverse_direction","forward_direction"){ $p_chr=$chromt; + #print "direction = $direct\n"; $p_chr = $p_chr."r" if $direct eq "reverse_direction"; $p_chr = $p_chr if $direct eq "forward_direction"; my $config = $species_set; $config=~s/,/./g; my @orgs = split(/\./,$arranged_species_set); + #print "ORGS= @orgs\n"; my @tag=@orgs; @@ -80,6 +95,7 @@ my $ptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1])."-".$threshold_array; my @sp_tags = (); + #print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n"; foreach my $sp (@tag){ push(@sp_tags, ($sp.".".$ptag)); } @@ -105,6 +121,10 @@ push(@title_queries, $title); } my $title_query = join($sep, @title_queries); + #print "title_queries=@title_queries\n"; + #print "query = >$title_query<\n"; + #print "orgs = @orgs\n"; + #------------------------------------------------------------------------------- # GET AXTNET FILES, EDIT THEM AND SPLIT THEM INTO HUMAN AND CHIMP INPUT FILES my $t1input = $pchr.".".$arranged_species_set.".net.axt"; @@ -115,6 +135,8 @@ } multi_species_t1($t1input,$tags,(join(",", @t1outputs)), $title_query); + #print "t1outputs=@t1outputs\n"; + #print "done t1\n"; #------------------------------------------------------------------------------- #START T2.PL @@ -261,6 +283,7 @@ multispecies_filtering_compound_microsats($compound_microsats, $compound_filterout, $compound_residue,$threshold_array,$threshold_array,scalar(@sp_tags)); $species_counter++; } + #print "done filtering both simple and compound microsatellites \n"; #------------------------------------------------------------------------------- @@ -289,6 +312,7 @@ } $sp_counter++; } + #print "\ndone grouping interrupted & simple microsats based on their motif size for further extention\n"; #------------------------------------------------------------------------------- # BREAK CHROMOSOME INTO PARTS OF CERTAIN NO. CONTIGS EACH, FOR FUTURE SEARCHING OF INTERRUPTED MICROSATELLITES @@ -311,6 +335,7 @@ my @unionarray = (); + #print "splist=@splist\n"; #------------------------------------------------------------------------------- # FIND INTERRUPTED MICROSATELLITES @@ -426,6 +451,7 @@ #xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx sub maftoAxt_multispecies { + #print "in maftoAxt_multispecies : got @_\n"; my $fname=$_[0]; open(IN,"<$_[0]") or die "Cannot open $_[0]: $! \n"; my $treedefinition = $_[1]; @@ -443,6 +469,7 @@ push @exactspecies, $spec if $spec eq $espec; } } + #print "exactspecies=@exactspecies\n"; ########### my $select = 2; @@ -453,7 +480,9 @@ my @allowedset = (); @allowedset = split(/;/,allowedSetOfSpecies(join("_",@species))) if $select == 0; @allowedset = join("_",0,@species) if $select == 1; + #print "species = @species , allowedset =",join("\n", @allowedset) ," \n"; @allowedset = join("_",0,@exactspecies) if $select == 2; + #print "allowedset = @allowedset and exactspecies = @exactspecies\n"; my $start = 0; my @sequences = (); @@ -474,6 +503,7 @@ } if ($line =~ /^s /){ + # print "fields1 = $fields[1] , start = $start\n"; foreach my $sp (@species){ if ($fields[1] =~ /$sp/){ @@ -493,12 +523,14 @@ my $arrno = 0; foreach my $set (@allowedset){ if ($arranged eq $set){ + # print "$arranged == $set\n"; $stopper = 0; last; } $arrno++; } if ($stopper == 0) { + # print " accepted\n"; @titles = split ";", orderInfo(join(";", @titles), $species_counter, $arranged) if $species_counter ne $arranged; @sequences = split ";", orderInfo(join(";", @sequences), $species_counter, $arranged) if $species_counter ne $arranged; my $filteredseq = filter_gaps(@sequences); @@ -519,6 +551,7 @@ } } +# print "countermatch = $countermatch\n"; } sub reorderSpecies{ @@ -535,6 +568,7 @@ sub filter_gaps{ my @sequences = @_; +# print "sequences sent are @sequences\n"; my $seq_length = length($sequences[0]); my $seq_no = scalar(@sequences); my $allgaps = (); @@ -557,7 +591,9 @@ for my $u (0 ... $#seq_array){ $bases = $bases.$seq_array[$u][$g]; } +# print $bases, "\n"; if ($bases eq $allgaps){ +# print "bases are $bases, position is $g \n"; for my $seq (@seq_array){ splice(@$seq , $g, 1); } @@ -580,6 +616,7 @@ sub allowedSetOfSpecies{ my @allowed_species = split(/_/,$_[0]); unshift @allowed_species, 0; +# print "allowed set = @allowed_species \n"; my @output = (); for (0 ... scalar(@allowed_species) - 4){ push(@output, join("_",@allowed_species)); @@ -626,14 +663,15 @@ my @fields = split(/\s*/,$line); $final_line = join("",reverse(@fields)); - print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; # $trycounter++; + # print "trying again....$trycounter : $final_line\n" if $final_line eq $line; # } } - print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; if ($line =~ /^[0-9]/){ - $line =~ s/chr([0-9a-b]+)/chr$1r/g; + $line =~ s/chr([A-Z0-9a-b]+)/chr$1r/g; $final_line = $line; } print OUT $final_line,"\n"; @@ -649,7 +687,7 @@ sub multi_species_t1 { my $input1 = $_[0]; - #print "@_\n"; #<STDIN>; +# print "@_\n"; #<STDIN>; my @tags = split(/_/, $_[1]); my @outputs = split(/,/, $_[2]); my $title_query = $_[3]; @@ -1678,7 +1716,7 @@ $key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12); } else{ - print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; +# print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; } if (exists $micros{$key}){ @@ -1686,8 +1724,8 @@ delete $micros{$key}; foreach my $line (@microstring){ - print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; - print "microsat = $line" if $printer == 1; +# print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; +# print "microsat = $line" if $printer == 1; $linecounter++; my $copy_line = $line; my @mields = split(/\t/,$line); @@ -1704,7 +1742,7 @@ my @microields = split(/\][a-zA-Z|-]*\[/,$microsatcopy); my @inields = split(/\[[a-zA-Z|-]*\]/,$microsat); my $absolutstart = 1; my $absolutend = $absolutstart + ($end-$start); - print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; +# print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; shift @inields; #print "inields =@inields<\n"; $motifline =~ s/^\[|\]$//gs; @@ -1790,11 +1828,11 @@ if ($rightstopper == 1 && $leftstopper == 1){ print COMP $line; - print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; +# print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; next; } - print "pased initial testing phase \n" if $printer == 1; +# print "pased initial testing phase \n" if $printer == 1; my @outputs = (); my @orig_starts = (); my @orig_ends = (); @@ -1845,7 +1883,7 @@ while($lefter == 1){ $newline = left_extender($templine, $seq,$org); - print "returned line from left extender= $newline \n" if $printer == 1; +# print "returned line from left extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} @@ -1853,7 +1891,7 @@ } while($righter == 1){ $newline = right_extender($templine, $seq,$org); - print "returned line from right extender= $newline \n" if $printer == 1; +# print "returned line from right extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} if (right_extention_permission_giver($templine) eq "no") {last;} @@ -1864,7 +1902,7 @@ my @tempmotields = split(/\]\[/,$tempfields[$motifcord]); if (scalar(@tempmotields) == 1 && $templine eq $orig_templine) { - print "scalar ( tempmotields) = 1\n" if $printer == 1; +# print "scalar ( tempmotields) = 1\n" if $printer == 1; next; } my $prevmotif = shift(@tempmotields); @@ -1877,7 +1915,7 @@ $prevmotif = $tempmot; } if ( $stopper == 1) { - print "length tempmot != length prevmotif\n" if $printer == 1; +# print "length tempmot != length prevmotif\n" if $printer == 1; next; } my $lastend = 0; @@ -1886,32 +1924,32 @@ my $left_bp = (); my $right_bp = (); # print "new startcord = $tempfields[$startcord] , new endcord = $tempfields[$endcord].. orig strts = @orig_starts and orig ends = @orig_ends\n"; for my $o (0 ... $#orig_starts){ - print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; - print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; if (($tempfields[$startcord] > $lastend) && ($tempfields[$startcord] <= $orig_ends[$o])){ # && ($tempfields[$startcord] != $fields[$startcord]) - print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; $left_captured = $o; $left_bp = $orig_ends[$o] - $tempfields[$startcord] + 1; } elsif ($tempfields[$endcord] > $lastend && $tempfields[$endcord] <= $orig_ends[$o]){ #&& $tempfields[$endcord] != $fields[$endcord]) - print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; $right_captured = $o; $right_bp = $tempfields[$endcord] - $orig_starts[$o] + 1; } $lastend = $orig_ends[$o] } - print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; +# print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; my $leftmotif = (); my $left_trashed = (); if ($tempfields[$startcord] != $fields[$startcord]) { $leftmotif = $motields[$left_captured]; - print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; +# print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; if ( $left_captured !~ /[0-9]+/) {print $line,"\n", $templine,"\n"; } $left_trashed = length($microields[$left_captured]) - $left_bp; } my $rightmotif = (); my $right_trashed = (); if ($tempfields[$endcord] != $fields[$endcord]) { - print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; +# print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; $rightmotif = $motields[$right_captured]; $right_trashed = length($microields[$right_captured]) - $right_bp; } @@ -1920,54 +1958,54 @@ $stopper = 0; my $deletioner = 0; #if($tempfields[$startcord] != $fields[$startcord]){ - print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; +# print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; if ($left_captured != 0){ - print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; +# print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; for my $e (0 ... $left_captured-1){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "after left search, deletioner = $deletioner\n" if $printer == 1; +# print "after left search, deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; next; } $deletioner = 0; #if($tempfields[$endcord] != $fields[$endcord]){ - print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; +# print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; if ($right_captured != $#microields){ - print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; +# print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; for my $e ($right_captured+1 ... $#microields){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e])) ){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { next; } @@ -1977,24 +2015,24 @@ if ($tempfields[$startcord] != $fields[$startcord] ){ #print "in left params: (length($leftmotif) == 1 && $tempfields[$startcord] != $fields[$startcord]) ... and .... $left_trashed > (1.5* length($leftmotif]) && ($tempfields[$startcord] != $fields[$startcord])\n"; if (length($leftmotif) == 1 && $left_trashed > 3){ - print "invaded left motif is long mononucleotide" if $printer == 1; +# print "invaded left motif is long mononucleotide" if $printer == 1; next; } elsif ((length($leftmotif) != 1 && $left_trashed > ( thrashallow($leftmotif)) && ($tempfields[$startcord] != $fields[$startcord]) ) ){ - print "invaded left motif too long" if $printer == 1; +# print "invaded left motif too long" if $printer == 1; next; } } if ($tempfields[$endcord] != $fields[$endcord] ){ #print "in right params: after $tempfields[$endcord] != $fields[$endcord] ..... (length($rightmotif)==1 && $tempfields[$endcord] != $fields[$endcord]) ... and ... $right_trashed > (1.5* length($rightmotif))\n"; if (length($rightmotif)==1 && $right_trashed){ - print "invaded right motif is long mononucleotide" if $printer == 1; +# print "invaded right motif is long mononucleotide" if $printer == 1; next; } elsif (length($rightmotif) !=1 && ($right_trashed > ( thrashallow($rightmotif)) && $tempfields[$endcord] != $fields[$endcord])){ - print "invaded right motif too long" if $printer == 1; +# print "invaded right motif too long" if $printer == 1; next; } @@ -2286,8 +2324,8 @@ ##print "scalar of fields = ",scalar(@fields),"\n"; if (exists ($fields[$motifcord+1])){ - print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; - <STDIN> if !exists $fields[$motifcord+1]; +# print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; +# <STDIN> if !exists $fields[$motifcord+1]; $fields[$motifcord+1] = $fields[$motifcord+1].",indel/deletion"; } else{$fields[$motifcord+1] = "indel/deletion";} @@ -2302,7 +2340,7 @@ my @seventeen=(); if (exists ($fields[$motifcord+3])){ ##print "at 608 we are doing this:length($microsat)+$intervalposs[$nikaal]\n"; - print " print fields = @fields\n " if !exists $fields[$motifcord+3]; +# print " print fields = @fields\n " if !exists $fields[$motifcord+3]; <STDIN> if !exists $fields[$motifcord+3]; my $currpos = length($microsat)+$intervalposs[$nikaal]; $fields[$motifcord+3] = $fields[$motifcord+3].",".$currpos; @@ -2596,7 +2634,7 @@ open(SUB,">$subset"); print SUB $sine; print OUT $subset,"\n"; - print $subset,"\n"; + # print $subset,"\n"; } } close OUT; @@ -2684,7 +2722,7 @@ my @microstring = @{$micros{$key}}; delete $micros{$key}; my @filteredmicrostring; - print "sequence = $sields[$sequencepos]" if $prinkter == 1; +# print "sequence = $sields[$sequencepos]" if $prinkter == 1; foreach my $line (@microstring){ $linecounter++; my $copy_line = $line; @@ -2692,7 +2730,7 @@ my $start = $fields[$startcord]; my $end = $fields[$endcord]; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; #LOOKING FOR LEFTWARD EXTENTION OF MICROSATELLITE my $newline; while(1){ @@ -2704,7 +2742,7 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_left_extention_permission_giver($line) eq "no") {last;} - print "returned line from left extender= $line \n" if $prinkter == 1; +# print "returned line from left extender= $line \n" if $prinkter == 1; } while(1){ # print "sequence = $sields[$sequencepos]\n" if $prinkter == 1; @@ -2715,9 +2753,9 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_right_extention_permission_giver($line) eq "no") {last;} - print "returned line from right extender= $line \n" if $prinkter == 1; +# print "returned line from right extender= $line \n" if $prinkter == 1; } - print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; +# print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; my @tempfields = split(/\t/,$line); if ($tempfields[$microsatcord] =~ /\[/){ @@ -2744,7 +2782,7 @@ sub multiSpecies_interruptedMicrosatHunter_left_extender{ my ($line, $seq, $org) = @_; - print "left extender, like passed = $line\n" if $prinkter == 1; +# print "left extender, like passed = $line\n" if $prinkter == 1; # print "in left extender... line passed = $line and sequence is $seq\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2763,7 +2801,7 @@ } else {$firstmotif = $motif;} - print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; my $leftphase = substr($microsat, 0,length($firstmotif)); my $phaser = $leftphase.$leftphase; my @phase = split(/\s*/,$leftphase); @@ -2779,7 +2817,7 @@ my $end = $rend; my $leftseq = substr($seq, 0, $start); - print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; +# print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2788,15 +2826,15 @@ my @intervals = (); my $firstmotif_length = length($firstmotif); foreach my $phase (@phases){ - print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; - print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; +# print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; +# print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; if ($leftseq =~ /(($phase)+([a-zA-Z|-]{0,$firstmotif_length}))$/i){ - print "in left pattern\n" if $prinkter == 1; +# print "in left pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = length($leftseq)-length($trapped); my $interval = $3; my $intervalpos = index($trapped, $interval) + 1; - print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1; +# print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1; my $extention = substr($trapped, 0, length($trapped)-length($interval)); my $leftpeep = substr($seq, 0, ($start-length($trapped))); @@ -2804,12 +2842,12 @@ for my $i (1 ... length($phase)-1){ my $overhang = substr($phase, -length($phase)+$i); - print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; +# print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; #TEMPORARY... BETTER METHOD NEEDED $leftpeep =~ s/-//g; if ($leftpeep =~ /$overhang$/i){ push(@passed_overhangs,$overhang); - print "l overhang\n" if $prinkter == 1; +# print "l overhang\n" if $prinkter == 1; } } @@ -2817,17 +2855,17 @@ my $overhang = $passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $overhang.$extention; $trapped = $overhang.$trapped; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; $trappedpos = length($leftseq)-length($trapped); } push(@extentions,$extention); - print "extentions = @extentions \n" if $prinkter == 1; +# print "extentions = @extentions \n" if $prinkter == 1; push(@trappeds,$trapped ); push(@intervalposs,length($extention)+1); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2837,7 +2875,7 @@ ############################ my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /\[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = "[".$trappedphases[$nikaal]."]".$fields[$motifcord]; @@ -2889,14 +2927,14 @@ if ($fields[$microsatcord] =~ /\[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline; } sub multiSpecies_interruptedMicrosatHunter_right_extender{ - print "right extender\n" if $prinkter == 1; +# print "right extender\n" if $prinkter == 1; my ($line, $seq, $org) = @_; - print "in right extender... line passed = $line\n" if $prinkter == 1; +# print "in right extender... line passed = $line\n" if $prinkter == 1; # print "line = $line, sequence = ",$seq, "\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2915,7 +2953,7 @@ } else {$temp_lastmotif = $motif;} my $lastmotif = substr($microsat,-length($temp_lastmotif)); - print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; my $rightphase = substr($microsat, -length($lastmotif)); my $phaser = $rightphase.$rightphase; my @phase = split(/\s*/,$rightphase); @@ -2931,8 +2969,8 @@ my $end = $rend; my $rightseq = substr($seq, $end+1); - print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; - print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; +# print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2941,15 +2979,15 @@ my @intervals = (); my $lastmotif_length = length($lastmotif); foreach my $phase (@phases){ - print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; - print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; +# print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; if ($rightseq =~ /^(([a-zA-Z|-]{0,$lastmotif_length}?)($phase)+)/i){ - print "in right pattern\n" if $prinkter == 1; +# print "in right pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = $end+1; my $interval = $2; my $intervalpos = index($trapped, $interval) + 1; - print "trapped = $trapped, interval = $interval\n" if $prinkter == 1; +# print "trapped = $trapped, interval = $interval\n" if $prinkter == 1; my $extention = substr($trapped, length($interval)); my $rightpeep = substr($seq, ($end+length($trapped))+1); @@ -2960,17 +2998,17 @@ for my $i (1 ... length($phase)-1){ my $overhang = substr($phase,0, $i); - print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; +# print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; if ($rightpeep =~ /^$overhang/i){ push(@passed_overhangs, $overhang); - print "r overhang\n" if $prinkter == 1; +# print "r overhang\n" if $prinkter == 1; } } if (scalar(@passed_overhangs) > 0){ my $overhang = @passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $extention.$overhang; $trapped = $trapped.$overhang; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; } push(@extentions,$extention); @@ -2979,7 +3017,7 @@ push(@trappeds,$trapped ); push(@intervalposs,$intervalpos); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2989,7 +3027,7 @@ ################################### my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /\[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = $fields[$motifcord]."[".$trappedphases[$nikaal]."]"; @@ -3032,7 +3070,7 @@ if ($fields[$microsatcord] =~ /\[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline; } @@ -3058,7 +3096,7 @@ #print "firststretch = $firststretch\n" if $prinkter == 1; } else {$firstmotif = $motif;$firststretch = $microsat;} - print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; +# print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; if (length($firststretch) < $thresholds[length($firstmotif)]){ return "no"; } @@ -3206,20 +3244,22 @@ } sub multiSpecies_interruptedMicrosatHunter_merge{ + $prinkter = 0; +# print "~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~\n"; my $line = $_[0]; - print "sent for mering: $line \n" if $prinkter ==1; +# print "sent for mering: $line \n" if $prinkter ==1; my @mields = split(/\t/,$line); my @fields = @mields; my $microsat = allCaps($fields[$microsatcord]); my $motifline = allCaps($fields[$motifcord]); my $microsatcopy = $microsat; - print "microsat = $microsat|\n" if $prinkter ==1; +# print "microsat = $microsat|\n" if $prinkter ==1; $microsatcopy =~ s/^\[|\]$//sg; chomp $microsatcopy; my @microields = split(/\][a-zA-Z|-]*\[/,$microsatcopy); my @inields = split(/\[[a-zA-Z|-]*\]/,$microsat); shift @inields; - print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; +# print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; $motifline =~ s/^\[|\]$//sg; my @motields = split(/\]\[/,$motifline); my @firstmotifs = (); @@ -3228,7 +3268,7 @@ $firstmotifs[$i] = substr($microields[$i],0,length($motields[$i])); $lastmotifs[$i] = substr($microields[$i],-length($motields[$i])); } - print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; +# print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; my @mergelist = (); my @inter_poses = split(/,/,$fields[$interr_poscord]); my $no_of_interruptions = $fields[$no_of_interruptionscord]; @@ -3236,52 +3276,56 @@ my @interrtypes = split(/,/,$fields[$interrtypecord]); my $stopper = 0; for my $i (0 ... $#motields-1){ - print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; +# print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; if ((allCaps($lastmotifs[$i]) eq allCaps($firstmotifs[$i+1])) && (!exists $inields[$i] || $inields[$i] !~ /[a-zA-Z]/)){ $stopper = 1; push(@mergelist, ($i)."_".($i+1)); #<STDIN> if $prinkter ==1; } } - print "mergelist = @mergelist\n" if $prinkter ==1; +# print "mergelist = @mergelist\n" if $prinkter ==1; return $line if scalar(@mergelist) == 0; - print "merging @mergelist\n" if $prinkter ==1; +# print "merging @mergelist\n" if $prinkter ==1; # <STDIN> if $prinkter ==1; foreach my $merging (@mergelist){ my @sets = split(/_/, $merging); - print "sets = @sets\n" if $prinkter ==1; +# print "sets = @sets\n" if $prinkter ==1; my @tempmicro = (); my @tempmot = (); - print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; +# print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; for my $i (0 ... $sets[0]-1){ - print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; +# print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; push(@tempmicro, "[".$microields[$i]."]"); push(@tempmicro, $inields[$i]); push(@tempmot, "[".$motields[$i]."]"); - print "adding pre-motifs number $i\n" if $prinkter ==1; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "adding pre-motifs number $i\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; } - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; my $pusher = "[".$microields[$sets[0]].$microields[$sets[1]]."]"; +# print "middle is, from @motields - @sets, number 0 which is is\n"; +# print ": $motields[$sets[0]]\n"; push (@tempmicro, $pusher); push(@tempmot, "[".$motields[$sets[0]]."]"); - push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields; + push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields && exists $sets[1] && exists $inields[$sets[1]]; my $outcoming = -2; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; for my $i ($sets[1]+1 ... $#microields){ - print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; - push(@tempmicro, "[".$microields[$i]."]"); - push(@tempmicro, $inields[$i]) unless $i == $#microields; +# print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; + push(@tempmicro, "[".$microields[$i]."]") if exists $microields[$i]; + push(@tempmicro, $inields[$i]) unless $i == $#microields || !exists $inields[$i]; push(@tempmot, "[".$motields[$i]."]"); - print "adding post-motifs number $i\n" if $prinkter ==1; +# print "adding post-motifs number $i\n" if $prinkter ==1; $outcoming = $i; } +# print "____________________________________________________________________________\n"; + $prinkter = 0; $fields[$microsatcord] = join("",@tempmicro); $fields[$motifcord] = join("",@tempmot); - print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; splice(@interrtypes, $sets[0], 1); $fields[$interrtypecord] = join(",",@interrtypes); @@ -3300,7 +3344,7 @@ else{ $line = join("\t", @fields); } - print "post merging, the line is $line\n" if $prinkter ==1; +# print "post merging, the line is $line\n" if $prinkter ==1; #<STDIN> if $stopper ==1; return $line; } @@ -3411,7 +3455,7 @@ while(my $sine = <SEQ>){ #<STDIN> if $sine =~ /16349128/; next if $sine !~ /[a-zA-Z0-9]/; - print "-" x 150, "\n" if $printer == 1; +# print "-" x 150, "\n" if $printer == 1; my @sields = split(/\t/,$sine); my @merged = (); @@ -3435,7 +3479,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$fmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3457,7 +3501,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$rmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3553,7 +3597,7 @@ my @mergedSet = (); # print "set of microsats = @microstring \n"; my @microstring = map { $_->[0] } sort custom map { [$_, split /\t/ ] } @microstring0; - print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; +# print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; #<STDIN> if $printer == 1; my @tempmicrostring = @microstring; foreach my $line (@tempmicrostring){ @@ -3567,7 +3611,7 @@ } my $firstflag = 'down'; while( my $line =shift(@microstring)){ - print "-----------\nline = $line \n" if $printer == 1; +# print "-----------\nline = $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3592,9 +3636,9 @@ my $endrank = 1; while( ($startflag eq "down") || ($endflag eq "down") ){ - print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; +# print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; if ( (($prestart < 0) && $firstflag eq "up") || (($postend > length($sequence) && $firstflag eq "up")) ){ - print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; +# print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; last; } @@ -3611,7 +3655,7 @@ chomp $startmicro; $flag = 'down'; $startrank++; - print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; delete $microend{$i}; delete $microstart{$tields[$startcord]}; $end = $tields[$endcord]; @@ -3629,7 +3673,7 @@ if ($endflag eq "down"){ for my $i ($start ... $postend){ - print "$start ----> $i -----> $postend\n" if $printer == 1; +# print "$start ----> $i -----> $postend\n" if $printer == 1; if(exists $microstart{$i} ){ chomp $microstart{$i}[0]; if(exists $compoundhash{$microstart{$i}[0]}) {next;} @@ -3640,11 +3684,11 @@ $endrank++; chomp $endmicro; $flag = 'down'; - print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; delete $microstart{$i} if exists $microstart{$i} ; delete $microend{$tields[$endcord]} if exists $microend{$tields[$endcord]}; - print "done\n" if $printer == 1; +# print "done\n" if $printer == 1; shift @microstring; $end = $tields[$endcord]; @@ -3656,25 +3700,25 @@ $flag = 'up'; $endflag = 'up'; } - print "out of the if\n" if $printer == 1; +# print "out of the if\n" if $printer == 1; } - print "out of the for\n" if $printer == 1; +# print "out of the for\n" if $printer == 1; } # print "for next turn, flag status: startflag = $startflag and endflag = $endflag \n"; } #end while( $flag eq "down") - print "compoundlines = @compoundlines \n" if $printer == 1; +# print "compoundlines = @compoundlines \n" if $printer == 1; if (scalar (@compoundlines) == 1){ push(@nonmerged, $line); } if (scalar (@compoundlines) > 1){ - print "FROM CLUSTERER\n" if $printer == 1; +# print "FROM CLUSTERER\n" if $printer == 1; push(@mergedSet,merge_microsats(@compoundlines, $sequence) ); } } #end foreach my $line (@microstring){ -print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; +# print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; #<STDIN> if scalar(@mergedSet) > 0; # print "EXIT: find_clusters\n"; return (join("_",@nonmerged). "=".join("_",@mergedSet)); @@ -3711,7 +3755,7 @@ my %forPopouting = (); while( my $line =shift(@merged)){ - print "\n MErgedline: $line \n" if $printer == 1; +# print "\n MErgedline: $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3764,7 +3808,7 @@ push(@mergedSet,join("\t",@compoundlines) ); } else { - print "FROM POPOUTER\n" if $printer == 1; +# print "FROM POPOUTER\n" if $printer == 1; push(@mergedSet, merge_microsats(@compoundlines, $sequence) ); } } @@ -3789,7 +3833,7 @@ $fields[$startcord] = $start; $fields[$endcord] = $end; $fields[$microsatcord] = reverse_micro($fields[$microsatcord]); - print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; +# print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; return join("\t",@fields); } @@ -3823,7 +3867,7 @@ my @fmerged = (); foreach my $micro (@merged) { my @fields = split(/\t/,$micro); - if ($fields[3] =~ /chr[0-9a-z]+r/){ + if ($fields[3] =~ /chr[A-Z0-9a-z]+r/){ my $key = join("_",$fields[1], $fields[$startcord], $fields[$endcord]); # print "adding ... \n$key\n$micro\n"; push(@{$revmerged{$key}}, $micro); @@ -3853,7 +3897,7 @@ sub invert_microsat{ my $micro = $_[0]; chomp $micro; - if ($micro =~ /chr[0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} + if ($micro =~ /chr[A-Z0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} else { $micro =~ s/chr([0-9a-b]+)/chr$1r/g ; } my $sequence = $_[1]; $sequence =~ s/ //g; @@ -4032,10 +4076,10 @@ foreach my $r (@localrs){ chomp $r; my @rields = split(/\t/,$r); - print "rields = @rields\n" if $printer == 1; +# print "rields = @rields\n" if $printer == 1; my $reciprocalstart = length($sequence) - $rields[$endcord] + 1; my $reciprocalend = length($sequence) - $rields[$startcord] + 1; - print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; +# print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; my $microsat = reverse_micro(all_caps($rields[$microsatcord])); my @localcollection=(); for my $i ($reciprocalstart+1 ... $reciprocalend-1){ @@ -4055,11 +4099,11 @@ } elsif (scalar(@localcollection) == 1){ - print "f microsat = $localcollection[0]\n" if $printer == 1; +# print "f microsat = $localcollection[0]\n" if $printer == 1; my @lields = split(/\t/,$localcollection[0]); $lields[$microsatcord]=all_caps($lields[$microsatcord]); - print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; - print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; +# print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; +# print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; if ($microsat eq $lields[$microsatcord]){ chomp $localcollection[0]; print SAME $localcollection[0], "\n"; @@ -4067,19 +4111,19 @@ if ($microsat ne $lields[$microsatcord]){ chomp $localcollection[0]; my $newmicro = microsatChooser(join("\t",@lields), join("\t",@rields), $sequence); - print "newmicro = $newmicro\n" if $printer == 1; +# print "newmicro = $newmicro\n" if $printer == 1; if ($newmicro =~ /[a-zA-Z]/){ print SAME $newmicro,"\n"; } else{ print DIFF join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n"; - print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; - print "@rields\n@lields\n" if $printer == 1; +# print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; +# print "@rields\n@lields\n" if $printer == 1; } } } else{ - print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; +# print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; } } } @@ -4146,13 +4190,13 @@ my $r_purestretch = join("",@r_microields); if ($fields[$typecord]=~/nucleotide/ && $rields[$typecord]=~/nucleotide/){ - print "now.. studying $forward\n$reverse\n" if $printer == 1; +# print "now.. studying $forward\n$reverse\n" if $printer == 1; if ($fields[$typecord] eq $rields[$typecord]){ - print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); @@ -4202,13 +4246,13 @@ } } if ($fields[$typecord] eq "compound" && $rields[$typecord] eq "compound"){ - print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; - print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; +# print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); return invert_microsat($reverse, $sequence) if $subset_answer == 0 && length($f_purestretch) < length($r_purestretch); if ($subset_answer == 3){ @@ -4243,11 +4287,11 @@ } if ($fields[$typecord] eq "compound" && $rields[$typecord] =~ /nucleotide/){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } if ($fields[$typecord] =~ /nucleotide/ && $rields[$typecord]eq "compound"){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } } @@ -4258,7 +4302,7 @@ my $seqLength = $_[2]; my $r_start = $seqLength - $rields[$endcord] + 1; my $r_end = $seqLength - $rields[$startcord] + 1; - print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; +# print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; return "0" if $fields[$startcord] == $r_start && $fields[$endcord] == $r_end; return "1" if $fields[$startcord] <= $r_start && $fields[$endcord] >= $r_end; return "2" if $r_start <= $fields[$startcord] && $r_end >= $fields[$endcord]; @@ -4284,7 +4328,7 @@ for my $i (0 ... $#sub){ my $probe = $sub[$i].$sub[$i]; - print "probing $probe and $mega[$i]\n" if $printer == 1; +# print "probing $probe and $mega[$i]\n" if $printer == 1; if ($probe =~ /$mega[$i]/) {$subresult = 1; } else {$subresult = 0; last; } } @@ -4416,7 +4460,7 @@ # print $key, "#-#-#-#-#-#-#-#\n"; if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { my $key = join("\t",$1, $2, $3, $4, $5); - print "key = $key\n" if $prinkter == 1; +# print "key = $key\n" if $prinkter == 1; push (@{$seen{$key}},$line); $microcounter++; } @@ -4424,7 +4468,7 @@ } } # print "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; - print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; +# print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; close SPUT; #---------------------------------------------------------------------------------------------------------------- @@ -4449,7 +4493,7 @@ my $keysused = 0; while (my $line = <MATCH>) { - print colored ['magenta'], $line if $prinkter == 1; +# print colored ['magenta'], $line if $prinkter == 1; next if $line !~ /[a-zA-Z0-9]/; chomp $line; my @fields2 = split(/\t/,$line); @@ -4458,10 +4502,10 @@ if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { $matchkeysformed++; $key2 = join("\t",$1, $2, $3, $4, $5); - print "key = $key2 \n" if $prinkter == 1; +# print "key = $key2 \n" if $prinkter == 1; } else{ - print "could not make ker in SEQ : $line\n"; +# print "could not make ker in SEQ : $line\n"; next; } my $sequence = $fields2[$sequencepos]; @@ -4473,7 +4517,7 @@ delete $seen{$key2}; my @sequencearr = split(/\s*/, $sequence); - print "sequencearr = @sequencearr\n" if $prinkter == 1; +# print "sequencearr = @sequencearr\n" if $prinkter == 1; my $counter; @@ -4487,13 +4531,13 @@ my @unsorted = (); my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} for my $u (0 ... $#unsorted_raw){ my @tields = split(/\t/,$unsorted_raw[$u]); next if exists $starts{$tields[$startcord]} && exists $ends{$tields[$endcord]}; push(@unsorted, $unsorted_raw[$u]); $starts{$tields[$startcord]} = $unsorted_raw[$u]; - print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; +# print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; } my $basecounter= 0; @@ -4517,7 +4561,7 @@ if (exists $starts{$basecounter}){ my $locus = $starts{$basecounter}; - print "locus identified = $locus\n" if $prinkter == 1; +# print "locus identified = $locus\n" if $prinkter == 1; my @fields3 = split(/\t/,$locus); my $start = $fields3[$startcord]; my $end = $fields3[$endcord]; @@ -4529,14 +4573,14 @@ my $leftbrackets=(); my $rightbrackets = (); my $micro_cpy = $microsat; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; while($microsat =~ m/\[/g) {push(@leftbracketpos, (pos($microsat))); $leftbrackets = join("__",@leftbracketpos);$bracket_picker='yes';} while($microsat =~ m/\]/g) {push(@rightbracketpos, (pos($microsat))); $rightbrackets = join("__",@rightbracketpos);} $microsat =~ s/[\[\]\-\*]//g; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; my $human_search = join '-*', split //, $microsat; my $temp = substr($sequence, $poscounter-1); - print "with poscounter = $poscounter\n" if $prinkter == 1; +# print "with poscounter = $poscounter\n" if $prinkter == 1; my $search_result = (); my $posnow = (); while ($temp =~ /($human_search)/gi){ @@ -4725,9 +4769,9 @@ if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key = join("\t",$1, $2, $4, $5); - print "key = : $key\n" if $prinkter == 1; +# print "key = : $key\n" if $prinkter == 1; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; push (@{$single_hash{$key}},$line); } else{ @@ -4736,10 +4780,10 @@ } push @hasharr, {%single_hash}; # print "@{$single_hash{$key}} \n"; - print "done $path: counter = $counter\n" if $prinkter == 1; +# print "done $path: counter = $counter\n" if $prinkter == 1; close READ; } - #print "Done hashes\n"; +# print "Done hashes\n"; #---------------------------------------------------------------------------------------------------------------- my $question=(); #---------------------------------------------------------------------------------------------------------------- @@ -4754,22 +4798,24 @@ my %contigpath=(); my $dotcounter = 0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; $dotcounter++; - #print "." if $dotcounter % 100 ==0; - #print "\n" if $dotcounter % 5000 ==0; +# print "." if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; next if $line !~ /^[0-9]+/; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; chomp $line; my @fields2 = split(/\t/,$line); my $key2 = (); if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key2 = join("\t",$1, $2, $4, $5); } - else {print "seq line $line incompatible\n" if $prinkter == 1; next;} + else { +# print "seq line $line incompatible\n" if $prinkter == 1; + next;} @@ -4809,22 +4855,22 @@ my @currentcontigchrs=(); for my $i (0 ... $#tags){ - print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; +# print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; my @temparr = (); if (exists $hasharr[$i]{$key2}){ @temparr = @{$hasharr[$i]{$key2}}; - print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; +# print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; $line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/; - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; +# print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $contigstarts[$i]{$startkey}= $key2; $contigends[$i]{$endkey}= $key2; - print "confirming existance: \n" if $prinkter == 1; - print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; - print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "confirming existance: \n" if $prinkter == 1; +# print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; $currentcontigchrs[$i]=$1; $currentcontigstarts[$i]=$2; $currentcontigends[$i]=$3; @@ -4846,7 +4892,7 @@ # print "---------------------------\n"; foreach my $templine (@temparr){ - print "templine = $templine\n" if $prinkter == 1; +# print "templine = $templine\n" if $prinkter == 1; my @tields = split(/\t/,$templine); my $start = $tields[$startcord]; # - $tields[$gapcord]; my $end = $tields[$endcord]; #- $tields[$gapcord]; @@ -4870,7 +4916,7 @@ foreach my $cluster (@clusters) { my @constituenst = split(/,/,$cluster); - print "clusters returned: @constituenst\n" if $prinkter == 1; +# print "clusters returned: @constituenst\n" if $prinkter == 1; } @string = split("_",stringPainter(join("_",@string),$foundclusters)); @@ -4879,13 +4925,13 @@ } next if $stopper == 1; - print colored ['blue'],"FINAL:\n" if $prinkter == 1; +# print colored ['blue'],"FINAL:\n" if $prinkter == 1; my $finalclusters =findClusters(join("!",@string), 1); - print colored ['blue'],"----------------------\n" if $prinkter == 1; +# print colored ['blue'],"----------------------\n" if $prinkter == 1; my @clusters = split(/,/,$finalclusters); - print "@string\n" if $prinkter == 1; - print "@clusters\n" if $prinkter == 1; - print "------------------------------------------------------------------\n" if $prinkter == 1; +# print "@string\n" if $prinkter == 1; +# print "@clusters\n" if $prinkter == 1; +# print "------------------------------------------------------------------\n" if $prinkter == 1; my $clustno = 0; @@ -4921,7 +4967,7 @@ my $extremeend = largest_number(@ends); push(@contigClusterstarts, $extremestart); push(@contigClusterends, $extremeend); - print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; +# print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; foreach my $clustparts (@localclust){ my @pattern = split(/:/, $clustparts); @@ -4929,7 +4975,7 @@ push (@result, $starthash[$pattern[0]]{$pattern[1]}); } push(@contigcluster, join("\t", @result)); - print join("\t", @result),"<-result \n" if $prinkter == 1 ; +# print join("\t", @result),"<-result \n" if $prinkter == 1 ; } @@ -4940,7 +4986,7 @@ $contigclustersFirstStartOnly{$key2}=$firstclusterstart; $contigclustersLastEndOnly{$key2} = $lastclusterend; $contigclusters{$key2}=[ @contigcluster ]; - print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; +# print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; for my $i (0 ... $#tags){ #1 check if there exists adjacent alignment block wrt coordinates of this species. next if $currentcontigchrs[$i] eq "0"; #1 this means that there are no microsats in this species in this alignment block.. @@ -4951,7 +4997,7 @@ #3 adjacent alignment block is found lateron, the exact distance between the potentially #4 adjacent microsat clusters can be found here. the exact start coordinate will be used #5 immediately below. - print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; + # print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; my $species_startsubstring = substr($origsequences[$i], 0, $firstclusterstart); my $species_endsubstring = (); @@ -4959,8 +5005,8 @@ if (length ($origsequences[$i]) <= $lastclusterend+1){ $species_endsubstring = "";} else{ $species_endsubstring = substr($origsequences[$i], $lastclusterend+1);} - print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; - print "for species: $tags[$i]: \n" if $prinkter == 1; +# print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; +# print "for species: $tags[$i]: \n" if $prinkter == 1; $species_startsubstring =~ s/-| //g; $species_endsubstring =~ s/-| //g; @@ -4969,11 +5015,11 @@ - print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; - print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; - print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; +# print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; +# print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; +# print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; - print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; +# print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; } @@ -5001,7 +5047,7 @@ my $existing_removed=0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; next if $line !~ /^[0-9]+/; #print $line; chomp $line; @@ -5012,7 +5058,7 @@ } else {print "seq line $line incompatible\n"; next;} - print "KEY = : $key2\n" if $prinkter == 1; +# print "KEY = : $key2\n" if $prinkter == 1; my @currentcontigstarts=(); @@ -5024,9 +5070,9 @@ @clusters = @{$contigclusters{$key2}}; @clusterscopy=@clusters; for my $i (0 ... $#tags){ - print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; + # print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; if ($line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/){ - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; + # print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $currentcontigchrs[$i]=$1; @@ -5035,7 +5081,7 @@ } else { $currentcontigchrs[$i] = 0; - print "no microsat clusters for $key2\n" if $prinkter == 1; next; + # print "no microsat clusters for $key2\n" if $prinkter == 1; next; } } } # print "exists: @{$hasharr[$i]{$key2}}[0]\n"} @@ -5050,7 +5096,7 @@ next if scalar @currentcontigchrs == 0; - print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; + # print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; my %visitedcontigs=(); for my $i (0 ... $#tags){ @@ -5067,38 +5113,38 @@ my $lastclusterend = $contigclustersLastEndOnly{$key2}; my $key3 = $currentcontigchrs[$i]."_".($currentcontigstarts[$i]); - print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; +# print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; if (exists($contigends[$i]{$key3}) && !exists $visitedcontigs{$contigends[$i]{$key3}}){ $visitedcontigs{$contigends[$i]{$key3}} = $contigends[$i]{$key3}; #1 this array keeps track of adjacent contigs that we have already visited, thus saving computational time and potential redundancies# - print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; + # print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; #1 extract coordinates of the last cluster of this found alignment block - print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; - print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; - print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; - print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; +# print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; + # print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; + # print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; + # print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; my @contigclustersAllFirstStartLengthOnly_raw=@{$contigclustersFirstStartLengthOnly{$key2}}; my @contigclustersAllLastEndLengthOnly_raw=@{$contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}}; my @contigclustersAllFirstStartLengthOnly=(); my @contigclustersAllLastEndLengthOnly=(); for my $val (0 ... $#contigclustersAllFirstStartLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllFirstStartLengthOnly_raw[$val]){ push(@contigclustersAllFirstStartLengthOnly, $contigclustersAllFirstStartLengthOnly_raw[$val]) if $contigclustersAllFirstStartLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "-----\n" if $prinkter == 1; + # print "-----\n" if $prinkter == 1; for my $val (0 ... $#contigclustersAllLastEndLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllLastEndLengthOnly_raw[$val]){ push(@contigclustersAllLastEndLengthOnly, $contigclustersAllLastEndLengthOnly_raw[$val]) if $contigclustersAllLastEndLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; - print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; + # print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; + # print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; # if ($contigclustersFirstStartLengthOnly{$key2}[$i] + $contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}[$i] < 50){ if (smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly) < $CLUSTER_DIST){ @@ -5119,7 +5165,7 @@ # print " clusteringpaths $key2 -> $contigends[$i]{$key3}\n"; $founkeys_enteredcount-- if exists $foundkeys{$key2}; $existing_removed++ if exists $foundkeys{$key2}; - print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; +# print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; delete $foundkeys{$key2} if exists $foundkeys{$key2}; $complete_transfered++; } @@ -5165,13 +5211,13 @@ my $pathed_count=0; foreach my $key2 (keys %foundkeys){ #print "x" x 60, "\n"; - print "x" if $dotcounter % 100 ==0; - print "\n" if $dotcounter % 5000 ==0; +# print "x" if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; $founkeys_count++; my $key = $key2; - print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; +# print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; if ($clusteringpaths{$key} eq $key){ - print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; +# print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; $nopath_count++; delete $foundkeys{$key2}; print ORTH join ("\n",@{$contigclusters{$key2}}),"\n"; @@ -5180,43 +5226,43 @@ my @pool=(); my $key3=(); $pathed_count++; - print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; - print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; if ($clusteringpathsRev{$key} eq "0") { next; } else{ my $yek3 = $clusteringpathsRev{$key}; my $yek = $key; - print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; +# print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; while ($yek3 ne "0"){ - print "$yek->$yek3," if $prinkter == 1; +# print "$yek->$yek3," if $prinkter == 1; $yek = $yek3; $yek3 = $clusteringpathsRev{$yek}; } - print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; +# print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; $key3 = $clusteringpaths{$yek}; $key = $yek; } - print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; +# print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; while($key ne $key3){ - print "KEEY $key->$key3\n" if $prinkter == 1; - print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; +# print "KEEY $key->$key3\n" if $prinkter == 1; +# print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; if (scalar(@{$contigclusters{$key}}) > 0) {push @pool, @{$contigclusters{$key}}; print "now pool = @pool\n" if $prinkter == 1;} delete $foundkeys{$key3}; $key=$key3; $key3=$clusteringpaths{$key}; } - print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; +# print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; my @firstcontig= @{$contigclusters{$key}}; delete $foundkeys{$key2} if exists $foundkeys{$key2} ; delete $foundkeys{$key} if exists $foundkeys{$key}; unshift @pool, pop @firstcontig; - print join("\t",@pool),"\n" if $prinkter == 1; +# print join("\t",@pool),"\n" if $prinkter == 1; print ORTH join ("\n",@firstcontig),"\n" if scalar(@firstcontig) > 0; print ORTH join ("\t",@pool),"\n"; # join(); @@ -5224,7 +5270,7 @@ } #close (NORTH); - print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; +# print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; close (BO); close (ORTH); close (OUTP); --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Thu Feb 10 10:33:08 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0"> +<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1"><description> for multiple (>2) species alignments</description><command interpreter="perl"> multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix for MySQL index lengths in migration script 62. Thanks Leandro Hermida.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/72cbd1ed1a81/ changeset: r5036:72cbd1ed1a81 user: natefoo date: 2011-02-09 22:49:43 summary: Fix for MySQL index lengths in migration script 62. Thanks Leandro Hermida. affected #: 1 file (1 byte) --- a/lib/galaxy/model/migrate/versions/0062_user_openid_table.py Wed Feb 09 16:46:30 2011 -0500 +++ b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py Wed Feb 09 16:49:43 2011 -0500 @@ -40,7 +40,7 @@ ix_name = 'ix_galaxy_user_openid_openid' if migrate_engine.name == 'mysql': - i = "ALTER TABLE galaxy_user_openid ADD UNIQUE INDEX ( openid( 1000 ) )" + i = "ALTER TABLE galaxy_user_openid ADD UNIQUE INDEX ( openid( 255 ) )" db_session.execute( i ) else: i = Index( ix_name, UserOpenID_table.c.openid, unique=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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