Mercurial > repos > earlhaminst > replace_chromosome_names
comparison replace_chromosome_names.py @ 0:97c11d04cd4c draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ commit 588282bf5cbb9909ad9cd8c316ec33158c858727
author | earlhaminst |
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date | Thu, 18 May 2017 14:17:48 -0400 |
parents | |
children | 6c0373cc070f |
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-1:000000000000 | 0:97c11d04cd4c |
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1 #!/usr/bin/env python | |
2 from __future__ import print_function | |
3 | |
4 import argparse | |
5 import sys | |
6 | |
7 | |
8 def main(): | |
9 parser = argparse.ArgumentParser(description='Replace chromosome names in a tabular (e.g. VCF) file using a mapping table.') | |
10 parser.add_argument('--cols', required=True, help='comma-separated list of column indexes (starting from 1) on which to perform the replacement') | |
11 parser.add_argument('-m', dest='mapping_file', type=argparse.FileType(), required=True, help='mapping table file. Must contain 2 tab-separated columns') | |
12 parser.add_argument('--comment-char', help='lines starting with this character will be directly printed to the output file') | |
13 parser.add_argument('-o', dest='output', type=argparse.FileType('w'), default=sys.stdout, help='output file. If not specified, writes on standard output') | |
14 parser.add_argument('input', metavar='INPUT', type=argparse.FileType(), help='tabular input file') | |
15 args = parser.parse_args() | |
16 | |
17 map_dict = dict() | |
18 for line in args.mapping_file: | |
19 line = line.rstrip('\r\n') | |
20 line_cols = line.split('\t') | |
21 if len(line_cols) < 2: | |
22 raise Exception("Line '%s' in mapping table file does not contain 2 tab-separated columns" % line) | |
23 map_dict[line_cols[0]] = line_cols[1] | |
24 | |
25 cols_to_map = [int(_) - 1 for _ in args.cols.split(',')] | |
26 | |
27 for line in args.input: | |
28 line = line.rstrip('\r\n') | |
29 if args.comment_char and line.startswith(args.comment_char): | |
30 print(line, file=args.output) | |
31 else: | |
32 line_cols = line.split('\t') | |
33 for col_to_map in cols_to_map: | |
34 old_value = line_cols[col_to_map] | |
35 line_cols[col_to_map] = map_dict.get(old_value, old_value) | |
36 mapped_line = '\t'.join(line_cols) | |
37 print(mapped_line, file=args.output) | |
38 | |
39 | |
40 if __name__ == "__main__": | |
41 main() |