# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1280945077 14400 # Node ID b7cf694b28c2461f652e76593f5fad088756d813 # Parent 77575a5f348d7d10c1df423c5faa71abaefd5f8a Update gops_intersect and gops_subtract documentation to reflect that tools can accept both BED and GFF files.

--- a/tools/new_operations/gops_subtract.py +++ b/tools/new_operations/gops_subtract.py @@ -1,9 +1,9 @@ #!/usr/bin/env python """ -Find regions of first bed file that do not overlap regions in a second -bed file +Find regions of first interval file that do not overlap regions in a second +interval file. Interval files can either be BED or GFF format.

-usage: %prog bed_file_1 bed_file_2 out_file +usage: %prog interval_file_1 interval_file_2 out_file -1, --cols1=N,N,N,N: Columns for start, end, strand in first file -2, --cols2=N,N,N,N: Columns for start, end, strand in second file -m, --mincols=N: Require this much overlap (default 1bp)

--- a/tools/new_operations/gops_intersect.py +++ b/tools/new_operations/gops_intersect.py @@ -1,8 +1,9 @@ #!/usr/bin/env python """ -Find regions of first interval/GFF file that overlap regions in a second interval/GFF file +Find regions of first interval file that overlap regions in a second interval file. +Interval files can either be BED or GFF format.

-usage: %prog bed_file_1 bed_file_2 out_file +usage: %prog interval_file_1 interval_file_2 out_file -1, --cols1=N,N,N,N: Columns for start, end, strand in first file -2, --cols2=N,N,N,N: Columns for start, end, strand in second file -m, --mincols=N: Require this much overlap (default 1bp)