# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks@emory.edu> # Date 1288027566 14400 # Node ID aaacde471f036ea236155b9786e095382b391a9f # Parent 141e7055d2c633afee5262932adb1896ad0f937e When converting from GFF to BED, make all BED features with thick blocks. --- a/tools/filters/gff_to_bed_converter.py +++ b/tools/filters/gff_to_bed_converter.py @@ -41,8 +41,12 @@ def get_bed_line( chrom, name, strand, b # Bed format: chrom, chromStart, chromEnd, name, score, strand, \ # thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts # + # Render complete feature with thick blocks. There's no clear way to do this unless + # we analyze the block names, but making everything thick makes more sense than + # making everything thin. + # return "%s\t%i\t%i\t%s\t0\t%s\t%i\t%i\t0\t%i\t%s\t%s\n" % \ - ( chrom, t_start, t_end, name, strand, t_start, t_start, len( block_starts ), + ( chrom, t_start, t_end, name, strand, t_start, t_end, len( block_starts ), ",".join( block_sizes ), ",".join( block_starts ) ) def __main__():