1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157/ changeset: 3c7416baa157 user: jgoecks date: 2011-08-15 01:49:26 summary: (1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool. affected #: 2 files (1.3 KB)

--- a/lib/galaxy/datatypes/util/gff_util.py Fri Aug 12 10:33:26 2011 +0100 +++ b/lib/galaxy/datatypes/util/gff_util.py Sun Aug 14 19:49:26 2011 -0400 @@ -87,6 +87,13 @@ intervals_copy.append( interval.copy() ) return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col, self.score_col, self.strand, intervals=intervals_copy ) + + def lines( self ): + lines = [] + for interval in self.intervals: + lines.append( '\t'.join( interval.fields ) ) + return lines +

class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): """ @@ -209,6 +216,10 @@ #finally: #raw_size += len( self.current_line )

+ # Ignore comments. + if isinstance( interval, Comment ): + continue + # If interval not associated with feature, break. group = interval.attributes.get( 'group', None ) # GFF test:

--- a/tools/extract/extract_genomic_dna.py Fri Aug 12 10:33:26 2011 +0100 +++ b/tools/extract/extract_genomic_dna.py Sun Aug 14 19:49:26 2011 -0400 @@ -14,6 +14,7 @@ pkg_resources.require( "bx-python" ) import sys, string, os, re, tempfile, subprocess from bx.cookbook import doc_optparse +from bx.intervals.io import Header, Comment import bx.seq.nib import bx.seq.twobit from galaxy.tools.util.galaxyops import * @@ -111,9 +112,17 @@ # # Fetch sequences. # + + # Get feature's line(s). + def get_lines( feature ): + if isinstance( feature, gff_util.GFFFeature ): + return feature.lines() + else: + return [ feature.rstrip( '\r\n' ) ] + skipped_lines = 0 first_invalid_line = 0 - invalid_line = '' + invalid_lines = [] fout = open( output_filename, "w" ) warnings = [] warning = '' @@ -121,7 +130,13 @@ file_iterator = open( input_filename ) if gff_format and interpret_features: file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False ) - for i, feature in enumerate( file_iterator ): + line_count = 1 + for feature in file_iterator: + # Ignore comments, headers. + if isinstance( feature, ( Header, Comment ) ): + line_count += 1 + continue + if gff_format and interpret_features: # Processing features. gff_util.convert_gff_coords_to_bed( feature ) @@ -145,18 +160,18 @@ 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 + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) 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 + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue

if strand not in ['+', '-']: @@ -174,13 +189,13 @@ nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: sequence = nib.get( start, end-start ) - except: + except Exception, e: 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 + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue elif seq_path and os.path.isfile( seq_path ): if not(twobitfile): @@ -194,29 +209,29 @@ else: sequence = twobitfile[chrom][start:end] except: - warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey ) + warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " %( start, end-start, chrom ) warnings.append( warning ) - skipped_lines += 1 - if not invalid_line: - first_invalid_line = i + 1 - invalid_line = line + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) 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 + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) 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 + if not invalid_lines: + invalid_lines = get_lines( feature ) + first_invalid_line = line_count + skipped_lines += len( invalid_lines ) continue if includes_strand_col and strand == "-": sequence = reverse_complement( sequence ) @@ -248,6 +263,12 @@ else: format_str = "%s\t%s\n" fout.write( format_str % ( meta_data, str( sequence ) ) ) + + # Update line count. + if isinstance( feature, gff_util.GFFFeature ): + line_count += len( feature.intervals ) + else: + line_count += 1

fout.close()

@@ -256,6 +277,7 @@ warn_msg += warnings[0] print warn_msg if skipped_lines: - print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + # Error message includes up to the first 10 skipped lines. + print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) )

if __name__ == "__main__": __main__()

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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