Mercurial > repos > devteam > merge
view gops_merge.py @ 5:dfbbc0291b36 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author | devteam |
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date | Thu, 22 Jun 2017 18:51:08 -0400 |
parents | b9c97d3233bb |
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#!/usr/bin/env python """ Merge overlapping regions. usage: %prog in_file out_file -1, --cols1=N,N,N,N: Columns for start, end, strand in first file -m, --mincols=N: Require this much overlap (default 1bp) -3, --threecol: Output 3 column bed """ 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.merge import merge 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(): mincols = 1 options, args = doc_optparse.parse( __doc__ ) try: chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) if options.mincols: mincols = int( options.mincols ) 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 ) out_file = open( out_fname, "w" ) try: for line in merge(g1, mincols=mincols): if options.threecol: if type( line ) is GenomicInterval: out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) ) elif type( line ) is list: out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) ) else: out_file.write( "%s\n" % line ) else: if type( line ) is GenomicInterval: out_file.write( "%s\n" % "\t".join( line.fields ) ) elif type( line ) is list: out_file.write( "%s\n" % "\t".join( line ) ) else: out_file.write( "%s\n" % line ) except ParseError as 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 __name__ == "__main__": main()