Mercurial > repos > devteam > intersect
diff gops_intersect.py @ 0:d4d33e26deef
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 09:13:16 -0400 |
parents | |
children | 4e321cae9da1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gops_intersect.py Tue Apr 01 09:13:16 2014 -0400 @@ -0,0 +1,95 @@ +#!/usr/bin/env python +""" +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 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) + -p, --pieces: just print pieces of second set (after padding) + -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 +""" +import sys, traceback, fileinput +from warnings import warn +from bx.intervals import * +from bx.intervals.io import * +from bx.intervals.operations.intersect import * +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * +from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + mincols = 1 + upstream_pad = 0 + downstream_pad = 0 + + options, args = doc_optparse.parse( __doc__ ) + try: + chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) + chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) + if options.mincols: mincols = int( options.mincols ) + pieces = bool( options.pieces ) + in1_gff_format = bool( options.gff1 ) + in2_gff_format = bool( options.gff2 ) + in_fname, in2_fname, out_fname = args + except: + doc_optparse.exception() + + # Set readers to handle either GFF or default format. + if in1_gff_format: + in1_reader_wrapper = GFFReaderWrapper + else: + in1_reader_wrapper = NiceReaderWrapper + if in2_gff_format: + in2_reader_wrapper = GFFReaderWrapper + else: + in2_reader_wrapper = NiceReaderWrapper + + g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ), + chrom_col=chr_col_1, + start_col=start_col_1, + end_col=end_col_1, + strand_col=strand_col_1, + fix_strand=True ) + if in1_gff_format: + # Intersect requires coordinates in BED format. + g1.convert_to_bed_coord=True + g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ), + chrom_col=chr_col_2, + start_col=start_col_2, + end_col=end_col_2, + strand_col=strand_col_2, + fix_strand=True ) + if in2_gff_format: + # Intersect requires coordinates in BED format. + g2.convert_to_bed_coord=True + + out_file = open( out_fname, "w" ) + try: + for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ): + if isinstance( feature, GFFFeature ): + # Convert back to GFF coordinates since reader converted automatically. + convert_bed_coords_to_gff( feature ) + for interval in feature.intervals: + out_file.write( "%s\n" % "\t".join( interval.fields ) ) + elif isinstance( feature, GenomicInterval ): + out_file.write( "%s\n" % "\t".join( feature.fields ) ) + else: + out_file.write( "%s\n" % feature ) + except ParseError, 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" ) + if g2.skipped > 0: + print skipped( g2, filedesc=" of 2nd dataset" ) + +if __name__ == "__main__": + main()