Mercurial > repos > iuc > gemini_gene_wise
diff test-data/util/shrink_simple_tab.py @ 4:a26f0a30df65 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author | iuc |
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date | Fri, 14 Dec 2018 12:55:02 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/util/shrink_simple_tab.py Fri Dec 14 12:55:02 2018 -0500 @@ -0,0 +1,61 @@ +from __future__ import print_function + +import argparse +from functools import partial + + +def keep_line(line, pos_cols, region): + fields = line.rstrip().split(b'\t') + if fields[pos_cols[0]] == region[0]: # same chromosome + if ( + region[1] < int(fields[pos_cols[1]]) < region[2] + ) or ( + region[1] < int(fields[pos_cols[2]]) < region[2] + ): + return True + + +def main(infile, ofile, num_header_lines): + print(infile, '->', ofile) + with open(infile, 'rb') as i: + with open(ofile, 'wb') as o: + # copy header lines + for c in range(num_header_lines): + o.write(next(i)) + for line in i: + if keep_line(line): + o.write(line) + + +if __name__ == '__main__': + p = argparse.ArgumentParser() + p.add_argument('infile') + p.add_argument( + '-r', '--region', + required=True, + help='the region of the input file to rewrite' + ) + p.add_argument( + '-o', '--ofile', + required=True, + help="the name of the output file" + ) + p.add_argument( + '-c', '--cols', + nargs=3, type=int, required=True, + help="the columns of the input file specifying chrom, start and stop, " + "respectively" + ) + p.add_argument( + '-n', '--num-header-lines', + type=int, default=0, + help='the number of header lines present in the input; These will ' + 'always be copied over to the new file.' + ) + args = vars(p.parse_args()) + + chrom, reg = args['region'].split(':') + region = [chrom.encode()] + [int(x) for x in reg.split('-')] + keep_line = partial(keep_line, pos_cols=args['cols'], region=region) + + main(args['infile'], args['ofile'], args['num_header_lines'])