Mercurial > repos > devteam > basecoverage
view gops_basecoverage.py @ 5:21898544368b draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author | devteam |
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date | Mon, 13 Jun 2022 16:20:48 +0000 |
parents | 2cedec3759e4 |
children | 9c5ff4695c97 |
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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 """ from __future__ import print_function import fileinput import sys from bx.cookbook import doc_optparse from bx.intervals.io import NiceReaderWrapper from bx.intervals.operations.base_coverage import base_coverage 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 ) 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 as 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()