Mercurial > repos > devteam > basecoverage
view gops_basecoverage.py @ 2:057d57cf718d
Added tool image.
author | devteam <devteam@galaxyproject.org> |
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date | Mon, 14 Apr 2014 09:00:27 -0400 |
parents | 3755ee8a74d7 |
children | c929b6540d07 |
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#!/usr/bin/env python """ Count total base coverage. usage: %prog in_file out_file -1, --cols1=N,N,N,N: Columns for start, end, strand in first file """ import sys, traceback, fileinput from warnings import warn from bx.intervals import * from bx.intervals.io import * from bx.intervals.operations.base_coverage import * from bx.cookbook import doc_optparse from galaxy.tools.util.galaxyops import * assert sys.version_info[:2] >= ( 2, 4 ) def main(): 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 ) in_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 ) try: bases = base_coverage(g1) except ParseError, exc: fail( "Invalid file format: %s" % str( exc ) ) out_file = open( out_fname, "w" ) out_file.write( "%s\n" % str( bases ) ) out_file.close() if g1.skipped > 0: print skipped( g1, filedesc="" ) if __name__ == "__main__": main()