Mercurial > repos > iuc > concoct_merge_cut_up_clustering
view 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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#!/usr/bin/env python import argparse import gzip import os import sys from collections import defaultdict from functools import partial import pandas as pd from Bio import SeqIO parser = argparse.ArgumentParser(description=__doc__) parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file") parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file") parser.add_argument("--output_path", help="Output directory") args = parser.parse_args() all_seqs = {} if args.gzipped: _open = partial(gzip.open, mode='rt') else: _open = open with _open(args.input_fasta) as fh: for seq in SeqIO.parse(fh, "fasta"): all_seqs[seq.id] = seq # Make sure we're reading the file as tabular! df = pd.read_csv(args.input_cluster, sep='\t') try: assert df.columns[0] == 'contig_id' assert df.columns[1] == 'cluster_id' except AssertionError: sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n") sys.exit(-1) cluster_to_contigs = defaultdict(list) for i, row in df.iterrows(): cluster_to_contigs[row['cluster_id']].append(row['contig_id']) for cluster_id, contig_ids in cluster_to_contigs.items(): output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id)) seqs = [all_seqs[contig_id] for contig_id in contig_ids] with open(output_file, 'w') as ofh: SeqIO.write(seqs, ofh, 'fasta')