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annotate extract_fasta_bins.py @ 0:06c0eb033025 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
author iuc
date Fri, 18 Feb 2022 14:18:11 +0000
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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1 #!/usr/bin/env python
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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3 import argparse
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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4 import gzip
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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5 import os
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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6 import sys
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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7 from collections import defaultdict
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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8 from functools import partial
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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10 import pandas as pd
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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11 from Bio import SeqIO
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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13 parser = argparse.ArgumentParser(description=__doc__)
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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15 parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped')
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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16 parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Input Fasta file")
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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17 parser.add_argument("--input_cluster", action="store", dest="input_cluster", help="Concoct output cluster file")
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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18 parser.add_argument("--output_path", help="Output directory")
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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20 args = parser.parse_args()
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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22 all_seqs = {}
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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23 if args.gzipped:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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24 _open = partial(gzip.open, mode='rt')
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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25 else:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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26 _open = open
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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28 with _open(args.input_fasta) as fh:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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29 for seq in SeqIO.parse(fh, "fasta"):
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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30 all_seqs[seq.id] = seq
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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32 # Make sure we're reading the file as tabular!
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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33 df = pd.read_csv(args.input_cluster, sep='\t')
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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34 try:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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35 assert df.columns[0] == 'contig_id'
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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36 assert df.columns[1] == 'cluster_id'
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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37 except AssertionError:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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38 sys.stderr.write("ERROR! Header line was not 'contig_id, cluster_id', please adjust your input file. Exiting!\n")
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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39 sys.exit(-1)
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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40
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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41 cluster_to_contigs = defaultdict(list)
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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42 for i, row in df.iterrows():
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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43 cluster_to_contigs[row['cluster_id']].append(row['contig_id'])
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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44
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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45 for cluster_id, contig_ids in cluster_to_contigs.items():
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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46 output_file = os.path.join(args.output_path, "{0}.fa".format(cluster_id))
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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47 seqs = [all_seqs[contig_id] for contig_id in contig_ids]
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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48 with open(output_file, 'w') as ofh:
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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49 SeqIO.write(seqs, ofh, 'fasta')