details: http://www.bx.psu.edu/hg/galaxy/rev/c81fa25c67e5 changeset: 1472:c81fa25c67e5 user: Greg Von Kuster <greg@bx.psu.edu> date: Tue Aug 19 10:44:08 2008 -0400 description: Some tool fixes: 1) fix for interval_maf_to_merged_fasta when strand column not included in input metadata 2) Tools using alignseq.loc now split on TAB rather than wihite space 3 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/maf/interval_maf_to_merged_fasta.py tools/metag_tools/blat_wrapper.py diffs (84 lines): diff -r 1958657d8f8d -r c81fa25c67e5 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 19 10:44:08 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue if fields[0] == dbkey: diff -r 1958657d8f8d -r c81fa25c67e5 tools/maf/interval_maf_to_merged_fasta.py --- a/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 19 10:44:08 2008 -0400 @@ -67,25 +67,29 @@ sys.exit() if not options.geneBED: - if options.chromCol: chr_col = int( options.chromCol ) - 1 + if options.chromCol: + chr_col = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column has not been specified." + print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.startCol: start_col = int( options.startCol ) - 1 + if options.startCol: + start_col = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column has not been specified." + print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.endCol: end_col = int( options.endCol ) - 1 + if options.endCol: + end_col = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column has not been specified." + print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.strandCol: strand_col = int( options.strandCol ) - 1 + if options.strandCol: + strand_col = int( options.strandCol ) - 1 else: - print >>sys.stderr, "Strand column has not been specified." - sys.exit() + strandCol = -1 + mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir #Finish parsing command line diff -r 1958657d8f8d -r c81fa25c67e5 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Tue Aug 19 10:44:08 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]