Mercurial > repos > iuc > gemini_pathways
view test-data/util/shrink_simple_tab.py @ 8:9551b3da9f5d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author | iuc |
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date | Wed, 13 Jul 2022 15:24:14 +0000 |
parents | 69b5327a1f88 |
children |
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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'])