1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/c6e1ef62c40b/ changeset: c6e1ef62c40b user: jgoecks date: 2012-08-09 23:32:47 summary: Data providers: unified and comprehensive handling of differences between different chromosome naming schemes. affected #: 1 file

diff -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 -r c6e1ef62c40b6c212210356fa59222b60645070b lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -44,6 +44,21 @@ if read[ end_pos_index ] > max_high: max_high = read[ end_pos_index ] return max_low, max_high + +def _convert_between_ucsc_and_ensemble_naming( chrom ): + ''' + Convert between UCSC chromosome ('chr1') naming conventions and Ensembl + naming conventions ('1') + ''' + if chrom.startswith( 'chr' ): + # Convert from UCSC to Ensembl + return chrom[ 3: ] + else: + # Convert from Ensembl to UCSC + return 'chr' + chrom + +def _chrom_naming_matches( chrom1, chrom2 ): + return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) )

class TracksDataProvider( object ): """ Base class for tracks data providers. """ @@ -159,7 +174,7 @@ return filters

def get_default_max_vals( self ): - return 5000; + return 5000

# # -- Base mixins and providers -- @@ -262,12 +277,9 @@

tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name)

- # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): - chrom = chrom[3:] + # If chrom not in data, try alternative. + if chrom not in tabix.contigs: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom )

return tabix.fetch(reference=chrom, start=start, end=end)

@@ -409,11 +421,6 @@ rval.append( payload ) continue

- # Simpler way to add stuff, but type casting is not done. - # Name, score, strand, thick start, thick end. - #end = min( len( feature ), 8 ) - #payload.extend( feature[ 3:end ] ) - # Name, strand, thick start, thick end. if length >= 4: payload.append(feature[3]) @@ -470,6 +477,14 @@ """

def get_iterator( self, chrom=None, start=None, end=None ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + def line_filter_iter(): for line in open( self.original_dataset.file_name ): if line.startswith( "track" ) or line.startswith( "browser" ): @@ -483,6 +498,7 @@ or ( end is not None and feature_end < start ): continue yield line + return line_filter_iter()

# @@ -601,6 +617,14 @@ """

def get_iterator( self, chrom, start, end ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + def line_filter_iter(): for line in open( self.original_dataset.file_name ): if line.startswith("#"): @@ -616,6 +640,7 @@ if variant_chrom != chrom or variant_start > end or variant_end < start: continue yield line + return line_filter_iter()

class SummaryTreeDataProvider( TracksDataProvider ): @@ -639,15 +664,11 @@ st = summary_tree_from_file( self.converted_dataset.file_name ) self.CACHE[filename] = st

- # If chrom is not found in blocks, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - if chrom in st.chrom_blocks: - pass - elif chrom[3:] in st.chrom_blocks: - chrom = chrom[3:] - else: - return None + # Look for chrom in tree using both naming conventions. + if chrom not in st.chrom_blocks: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + if chrom not in st.chrom_blocks: + return None

# Get or compute level. if level: @@ -684,7 +705,7 @@ self.CACHE[filename] = st

# Check for data. - return st.chrom_blocks.get(chrom, None) is not None or (chrom and st.chrom_blocks.get(chrom[3:], None) is not None) + return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None)

class BamDataProvider( TracksDataProvider, FilterableMixin ): """ @@ -727,13 +748,11 @@ try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: - # Some BAM files do not prefix chromosome names with chr, try without - if chrom.startswith( 'chr' ): - try: - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except ValueError: - return None - else: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: return None

# Write reads in region. @@ -757,13 +776,11 @@ try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: - # Some BAM files do not prefix chromosome names with chr, try without - if chrom.startswith( 'chr' ): - try: - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except ValueError: - return None - else: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: return None return data

@@ -1034,12 +1051,9 @@ source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name )

- # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in index.indexes and chrom[3:] in index.indexes: - chrom = chrom[3:] + if chrom not in index.indexes: + # Try alternative naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom )

return index.find(chrom, start, end)

@@ -1091,6 +1105,14 @@ a file offset. """ source = open( self.original_dataset.file_name ) + + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 )

def features_in_region_iter(): offset = 0 @@ -1100,6 +1122,7 @@ if feature.chrom == chrom and feature_end > start and feature_start < end: yield feature, offset offset += feature.raw_size + return features_in_region_iter()

def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):

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