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annotate misc/msa_sscs_matcher.py @ 4:af383638de66 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 18:44:23 -0500
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 import sys
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4 import argparse
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5
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6 OPT_DEFAULTS = {}
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7 USAGE = "gunzip -c families.msa.tsv.gz | %(prog)s sscs.set.fa"
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8 DESCRIPTION = """Find the input MSA's which produced a given set of SSCS's. Pipe the full set of
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9 MSA's to stdin and it will filter them to the matching MSA's on stdout."""
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11
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12 def main(argv):
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13
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14 parser = argparse.ArgumentParser(usage=USAGE, description=DESCRIPTION)
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15 parser.set_defaults(**OPT_DEFAULTS)
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16
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17 parser.add_argument('sscs', metavar='sscs.set.fa',
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18 help='A set of SSCS\'s, as output from the duplex.py script with the --sscs-file option.')
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19
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20 args = parser.parse_args(argv[1:])
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21
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22 sscs = set()
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23 with open(args.sscs) as sscs_file:
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24 for line in sscs_file:
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25 if line.startswith('>'):
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26 name = line.lstrip('>').split()[0]
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27 sscs.add(name)
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29 for line in sys.stdin:
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30 barcode, order, mate, rname, seq, qual = line.rstrip('\r\n').split('\t')
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31 name = '.'.join((barcode, order, mate))
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32 if name in sscs:
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33 sys.stdout.write(line)
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36 if __name__ == '__main__':
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37 sys.exit(main(sys.argv))