Mercurial > repos > devteam > coverage
view gops_coverage.py @ 2:7b226a8a6722 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:50:01 -0400 |
parents | 6b81ee6c18d3 |
children | ad25eb2c422d |
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#!/usr/bin/env python """ Calculate coverage of one query on another, and append the coverage to the last two columns as bases covered and percent coverage. usage: %prog bed_file_1 bed_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 """ import fileinput import sys from bx.intervals.io import GenomicInterval, NiceReaderWrapper from bx.intervals.operations.coverage import coverage from bx.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped assert sys.version_info[:2] >= ( 2, 4 ) def main(): 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 ) in_fname, in2_fname, out_fname = args except: doc_optparse.exception() g1 = NiceReaderWrapper( 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 ) g2 = NiceReaderWrapper( 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 ) out_file = open( out_fname, "w" ) try: for line in coverage( [g1, g2] ): if type( line ) is GenomicInterval: out_file.write( "%s\n" % "\t".join( line.fields ) ) else: out_file.write( "%s\n" % line ) except ParseError, exc: out_file.close() fail( "Invalid file format: %s" % str( exc ) ) 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()