Mercurial > repos > iuc > concoct

annotate merge_cut_up_clustering.py @ 2:7a145c72d375 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author iuc
date Fri, 01 Jul 2022 14:14:44 +0000
parents 031f84cb2fd3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
iuc
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1 #!/usr/bin/env python
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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3 import argparse
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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4 import re
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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5 import sys
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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6 from collections import Counter
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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7 from collections import defaultdict
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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10 CONTIG_PART_EXPR = re.compile(r'(.*)\.concoct_part_([0-9]*)')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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13 def original_contig_name_special(contig_id):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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14 try:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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15 original_id, part_index = CONTIG_PART_EXPR.match(contig_id).group(1, 2)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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16 return original_id, part_index
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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17 except AttributeError:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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18 # No matches for concoct_part regex.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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19 return contig_id, 0
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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22 parser = argparse.ArgumentParser()
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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23 parser.add_argument("--input", action="store", dest="input", help="Tabular file with cut up clusters")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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24 parser.add_argument("--output", action="store", dest="output", help="Output file with merged clusters")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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26 args = parser.parse_args()
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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27
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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28 # Get cut up clusters
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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29 all_seqs = {}
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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30 all_originals = defaultdict(dict)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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31 with open(args.input, 'r') as ifh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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32 for i, line in enumerate(ifh):
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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33 if i == 0:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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34 if 'contig_id' not in line:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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35 sys.stderr.write("ERROR nvalid clustering file, 'contig_id' is not found in the header.")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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36 sys.exit(-1)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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37 # Skip header.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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38 continue
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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39 line = line.rstrip('\r\n')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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40 contig_id, cluster_id = line.split('\t')
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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41 original_contig_name, part_id = original_contig_name_special(contig_id)
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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42 all_originals[original_contig_name][part_id] = cluster_id
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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43
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44 # Merge cut up clusters.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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45 with open(args.output, 'w') as ofh:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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46 ofh.write("contig_id\tcluster_id\n")
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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47 for original_contig_id, part_ids_d in all_originals.items():
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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48 if len(part_ids_d) > 1:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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49 c = Counter(part_ids_d.values())
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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50 cluster_id = c.most_common(1)[0][0]
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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51 c_string = [(a, b) for a, b in c.items()]
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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52 # Here if len(c.values()) > 1,
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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53 # then no cluster for contig.
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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54 else:
031f84cb2fd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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55 cluster_id = list(part_ids_d.values())[0]
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56 ofh.write(f"{original_contig_id}\t{cluster_id}\n")