Mercurial > repos > iuc > concoct_merge_cut_up_clustering
comparison extract_fasta_bins.py @ 0:b546422c9128 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 08:44:34 +0000 |
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-1:000000000000 | 0:b546422c9128 |
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1 #!/usr/bin/env python | |
2 | |
3 import argparse | |
4 import gzip | |
5 import os | |
6 import sys | |
7 from collections import defaultdict | |
8 from functools import partial | |
9 | |
10 import pandas as pd | |
11 from Bio import SeqIO | |
12 | |
13 parser = argparse.ArgumentParser(description=__doc__) | |
14 | |
15 parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') | |
16 parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file") | |
17 parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file") | |
18 parser.add_argument("--output_path", help="Output directory") | |
19 | |
20 args = parser.parse_args() | |
21 | |
22 all_seqs = {} | |
23 if args.gzipped: | |
24 _open = partial(gzip.open, mode='rt') | |
25 else: | |
26 _open = open | |
27 | |
28 with _open(args.input_fasta) as fh: | |
29 for seq in SeqIO.parse(fh, "fasta"): | |
30 all_seqs[seq.id] = seq | |
31 | |
32 # Make sure we're reading the file as tabular! | |
33 df = pd.read_csv(args.input_cluster, sep='\t') | |
34 try: | |
35 assert df.columns[0] == 'contig_id' | |
36 assert df.columns[1] == 'cluster_id' | |
37 except AssertionError: | |
38 sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n") | |
39 sys.exit(-1) | |
40 | |
41 cluster_to_contigs = defaultdict(list) | |
42 for i, row in df.iterrows(): | |
43 cluster_to_contigs[row['cluster_id']].append(row['contig_id']) | |
44 | |
45 for cluster_id, contig_ids in cluster_to_contigs.items(): | |
46 output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id)) | |
47 seqs = [all_seqs[contig_id] for contig_id in contig_ids] | |
48 with open(output_file, 'w') as ofh: | |
49 SeqIO.write(seqs, ofh, 'fasta') |