Mercurial > repos > iuc > tn93_readreduce

comparison tn93_filter.py @ 1:84849140a3bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author iuc
date Fri, 23 Apr 2021 03:04:45 +0000
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children 1d2ec0b0a0a7
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0:bdaadfd0c843 1:84849140a3bc
1 import argparse
2 import csv
3
4 from Bio import SeqIO
5
6 arguments = argparse.ArgumentParser(description='Combine alignments into a single file, adding a reference sequence as well')
7
8 arguments.add_argument('-f', '--reference', help='Reference sequence', required=True, type=str)
9 arguments.add_argument('-d', '--distances', help='Calculated pairwise distances', required=True, type=str)
10 arguments.add_argument('-r', '--reads', help='Output file for filtered reads', required=True, type=str)
11 arguments.add_argument('-q', '--clusters', help='Compressed clusters', required=True, type=str)
12 settings = arguments.parse_args()
13
14 reference_name = 'REFERENCE'
15 reference_seq = ''
16
17 with open(settings.reference) as seq_fh:
18 for seq_record in SeqIO.parse(seq_fh, 'fasta'):
19 reference_name = seq_record.name
20 reference_seq = seq_record.seq
21 break
22
23 with open(settings.distances) as fh:
24 reader = csv.reader(fh, delimiter=',')
25 next(reader)
26 seqs_to_filter = set()
27 for line in reader:
28 if line[1] not in seqs_to_filter:
29 seqs_to_filter.add(line[1])
30 if reference_name in seqs_to_filter:
31 seqs_to_filter.remove(reference_name)
32
33 with open(settings.reads, "a+") as fh:
34 seqs_filtered = list()
35 for seq_record in SeqIO.parse(settings.clusters, "fasta"):
36 if seq_record.name not in seqs_to_filter:
37 if seq_record.name == reference_name:
38 if seq_record.name not in seqs_filtered:
39 seqs_filtered.append(seq_record.name)
40 else:
41 continue
42 if reference_name not in seqs_filtered:
43 fh.write('\n>REFERENCE\n%s' % reference_seq)