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annotate tn93_filter.py @ 2:b38f620a3628 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
author iuc
date Wed, 20 Apr 2022 16:59:49 +0000
parents 9d793e88e15f
children
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9d793e88e15f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
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1 import argparse
9d793e88e15f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
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2 import csv
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b38f620a3628 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
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3 import random
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iuc
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5 from Bio import SeqIO
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7 arguments = argparse.ArgumentParser(description='Combine alignments into a single file, adding a reference sequence as well')
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9 arguments.add_argument('-f', '--reference', help='Reference sequence', required=True, type=str)
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10 arguments.add_argument('-d', '--distances', help='Calculated pairwise distances', required=True, type=str)
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11 arguments.add_argument('-r', '--reads', help='Output file for filtered reads', required=True, type=str)
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12 arguments.add_argument('-q', '--clusters', help='Compressed background clusters', required=True, type=str)
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13 settings = arguments.parse_args()
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15 reference_name = 'REFERENCE'
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16 reference_seq = ''
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19 def unique_id(new_id, existing_ids):
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20 while new_id in existing_ids:
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21 new_id += '_' + ''.join(random.choices('0123456789abcdef', k=10))
b38f620a3628 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
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22 return new_id
b38f620a3628 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
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25 with open(settings.reference) as seq_fh:
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26 for seq_record in SeqIO.parse(seq_fh, 'fasta'):
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27 reference_name = seq_record.name.split(' ')[0]
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28 reference_seq = seq_record.seq
9d793e88e15f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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29 break
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31 with open(settings.distances) as fh:
9d793e88e15f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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32 reader = csv.reader(fh, delimiter=',')
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33 next(reader)
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34 seqs_to_filter = set()
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35 for line in reader:
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36 if line[1] not in seqs_to_filter:
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37 seqs_to_filter.add(line[1])
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38 else:
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39 seqs_to_filter.add(unique_id(line[1], seqs_to_filter))
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40 if reference_name in seqs_to_filter:
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41 seqs_to_filter.remove(reference_name)
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43 with open(settings.reads, "a+") as fh:
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44 seqs_filtered = list()
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45 for seq_record in SeqIO.parse(settings.clusters, "fasta"):
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46 if seq_record.name.split(' ')[0] == reference_name:
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47 continue
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48 if seq_record.name not in seqs_to_filter:
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49 unique_name = unique_id(seq_record.name, seqs_filtered)
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50 fh.write('\n>%s\n%s' % (unique_name, seq_record.seq))
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51 seqs_filtered.append(unique_name)
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52 if reference_name not in seqs_filtered:
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53 fh.write('\n>REFERENCE\n%s' % reference_seq)