Mercurial > repos > devteam > intersect
diff gops_intersect.py @ 5:33b3f3688db4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author | devteam |
---|---|
date | Thu, 22 Jun 2017 18:52:23 -0400 |
parents | 5f72be09cfd3 |
children |
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--- a/gops_intersect.py Thu Feb 11 12:11:25 2016 -0500 +++ b/gops_intersect.py Thu Jun 22 18:52:23 2017 -0400 @@ -11,14 +11,18 @@ -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval """ +from __future__ import print_function + import fileinput import sys + +from bx.cookbook import doc_optparse from bx.intervals.io import GenomicInterval, NiceReaderWrapper from bx.intervals.operations.intersect import intersect -from bx.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped -from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff + +from utils.gff_util import convert_bed_coords_to_gff, GFFFeature, GFFReaderWrapper assert sys.version_info[:2] >= ( 2, 4 ) @@ -80,16 +84,17 @@ out_file.write( "%s\n" % "\t".join( feature.fields ) ) else: out_file.write( "%s\n" % feature ) - except ParseError, e: + except ParseError as e: out_file.close() fail( "Invalid file format: %s" % str( e ) ) out_file.close() if g1.skipped > 0: - print skipped( g1, filedesc=" of 1st dataset" ) + print(skipped( g1, filedesc=" of 1st dataset" )) if g2.skipped > 0: - print skipped( g2, filedesc=" of 2nd dataset" ) + print(skipped( g2, filedesc=" of 2nd dataset" )) + if __name__ == "__main__": main()