Mercurial > repos > iuc > tn93_cluster
view tn93_filter.py @ 0:af03f3398f03 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author | iuc |
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date | Fri, 23 Apr 2021 03:04:15 +0000 |
parents | |
children | 112d80c9ccca |
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import argparse import csv from Bio import SeqIO arguments = argparse.ArgumentParser(description='Combine alignments into a single file, adding a reference sequence as well') arguments.add_argument('-f', '--reference', help='Reference sequence', required=True, type=str) arguments.add_argument('-d', '--distances', help='Calculated pairwise distances', required=True, type=str) arguments.add_argument('-r', '--reads', help='Output file for filtered reads', required=True, type=str) arguments.add_argument('-q', '--clusters', help='Compressed clusters', required=True, type=str) settings = arguments.parse_args() reference_name = 'REFERENCE' reference_seq = '' with open(settings.reference) as seq_fh: for seq_record in SeqIO.parse(seq_fh, 'fasta'): reference_name = seq_record.name reference_seq = seq_record.seq break with open(settings.distances) as fh: reader = csv.reader(fh, delimiter=',') next(reader) seqs_to_filter = set() for line in reader: if line[1] not in seqs_to_filter: seqs_to_filter.add(line[1]) if reference_name in seqs_to_filter: seqs_to_filter.remove(reference_name) with open(settings.reads, "a+") as fh: seqs_filtered = list() for seq_record in SeqIO.parse(settings.clusters, "fasta"): if seq_record.name not in seqs_to_filter: if seq_record.name == reference_name: if seq_record.name not in seqs_filtered: seqs_filtered.append(seq_record.name) else: continue if reference_name not in seqs_filtered: fh.write('\n>REFERENCE\n%s' % reference_seq)