diff extract_fasta_bins.py @ 0:1bc8fd1b3ed0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fasta_bins.py	Fri Feb 18 14:17:48 2022 +0000
@@ -0,0 +1,49 @@
+#!/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')