opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

When converting from GFF to BED, make all BED features with thick blocks.

Browse Source
This commit is contained in:
Jeremy Goecks
2010-10-25 13:26:06 -04:00
parent 40172730ab
commit a9520cc626
1 changed files with 5 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/filters/gff_to_bed_converter.py
+5 -1
View File
@@ -41,8 +41,12 @@ def get_bed_line( chrom, name, strand, blocks ):
# 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__():