Mercurial > repos > iuc > concoct
comparison merge_cut_up_clustering.py @ 1:031f84cb2fd3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
author | iuc |
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date | Sun, 13 Mar 2022 08:45:05 +0000 |
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0:06c0eb033025 | 1:031f84cb2fd3 |
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1 #!/usr/bin/env python | |
2 | |
3 import argparse | |
4 import re | |
5 import sys | |
6 from collections import Counter | |
7 from collections import defaultdict | |
8 | |
9 | |
10 CONTIG_PART_EXPR = re.compile(r'(.*)\.concoct_part_([0-9]*)') | |
11 | |
12 | |
13 def original_contig_name_special(contig_id): | |
14 try: | |
15 original_id, part_index = CONTIG_PART_EXPR.match(contig_id).group(1, 2) | |
16 return original_id, part_index | |
17 except AttributeError: | |
18 # No matches for concoct_part regex. | |
19 return contig_id, 0 | |
20 | |
21 | |
22 parser = argparse.ArgumentParser() | |
23 parser.add_argument("--input", action="store", dest="input", help="Tabular file with cut up clusters") | |
24 parser.add_argument("--output", action="store", dest="output", help="Output file with merged clusters") | |
25 | |
26 args = parser.parse_args() | |
27 | |
28 # Get cut up clusters | |
29 all_seqs = {} | |
30 all_originals = defaultdict(dict) | |
31 with open(args.input, 'r') as ifh: | |
32 for i, line in enumerate(ifh): | |
33 if i == 0: | |
34 if 'contig_id' not in line: | |
35 sys.stderr.write("ERROR nvalid clustering file, 'contig_id' is not found in the header.") | |
36 sys.exit(-1) | |
37 # Skip header. | |
38 continue | |
39 line = line.rstrip('\r\n') | |
40 contig_id, cluster_id = line.split('\t') | |
41 original_contig_name, part_id = original_contig_name_special(contig_id) | |
42 all_originals[original_contig_name][part_id] = cluster_id | |
43 | |
44 # Merge cut up clusters. | |
45 with open(args.output, 'w') as ofh: | |
46 ofh.write("contig_id\tcluster_id\n") | |
47 for original_contig_id, part_ids_d in all_originals.items(): | |
48 if len(part_ids_d) > 1: | |
49 c = Counter(part_ids_d.values()) | |
50 cluster_id = c.most_common(1)[0][0] | |
51 c_string = [(a, b) for a, b in c.items()] | |
52 # Here if len(c.values()) > 1, | |
53 # then no cluster for contig. | |
54 else: | |
55 cluster_id = list(part_ids_d.values())[0] | |
56 ofh.write(f"{original_contig_id}\t{cluster_id}\n") |