1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5b0edf34839e/ changeset: r5268:5b0edf34839e user: richard_burhans date: 2011-03-24 20:03:12 summary: fixed calculation of codon starts affected #: 1 file (59 bytes) --- a/tools/filters/ucsc_gene_bed_to_exon_bed.py Thu Mar 24 14:33:05 2011 -0400 +++ b/tools/filters/ucsc_gene_bed_to_exon_bed.py Thu Mar 24 15:03:12 2011 -0400 @@ -103,13 +103,12 @@ i+=1 #for non-intron regions: else: - shift = 0 for start, end in zip( exon_starts, exon_ends ): start = max( start, region_start ) end = min( end, region_end ) if start < end: if options.region == 'codon': - start += shift + start += (3 - ((start-region_start)%3))%3 c_start = start while c_start+3 <= end: if strand: @@ -117,7 +116,6 @@ else: print_tab_sep(out_file, chrom, c_start, c_start+3) c_start += 3 - shift = (3 - ((end-start)%3))%3 else: if strand: print_tab_sep(out_file, chrom, start, end, name, "0", strand ) 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.