Mercurial > repos > iuc > ivar_variants

annotate write_amplicon_info_file.py @ 8:aea7008fe1f1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
author iuc
date Thu, 05 Aug 2021 12:44:05 +0000
parents
children 3888bbe7a9ca
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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1 #!/usr/bin/env python
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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3 import argparse
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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4 import re
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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6 AMPLICON_NAME_RE = r'.*_(?P<num>\d+)_[^0-9]*(?P<name>L(?:EFT)?|R(?:IGHT)?)'
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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9 def primer_info_to_position(name):
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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10 position = 0
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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11 re_match = re.match(AMPLICON_NAME_RE, name)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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12 if re_match is None:
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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13 raise ValueError("{} does not match expected amplicon name format".format(name))
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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14 side = re_match.group('name')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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15 num = re_match.group('num')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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16 if side == 'RIGHT' or side == 'R':
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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17 position += 1000
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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18 if num is not None:
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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19 position += int(num)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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20 return position
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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23 def write_amplicon_info_file(bed_file, amplicon_info_file):
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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24 amplicon_sets = {}
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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25 amplicon_ids = set()
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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26 for line in bed_file:
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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27 fields = line.strip().split('\t')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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28 name = fields[3]
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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29 re_match = re.match(AMPLICON_NAME_RE, name)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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30 if re_match is None:
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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31 raise ValueError("{} does not match expected amplicon name format".format(name))
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
iuc
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32 amplicon_id = int(re_match.group('num'))
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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33 amplicon_set = amplicon_sets.get(amplicon_id, [])
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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34 amplicon_set.append(name)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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35 amplicon_sets[amplicon_id] = amplicon_set
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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36 amplicon_ids.add(amplicon_id)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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38 for id in sorted(list(amplicon_ids)):
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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39 amplicon_info = '\t'.join([name for name in sorted(amplicon_sets[id], key=primer_info_to_position)]) + '\n'
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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40 amplicon_info_file.write(amplicon_info)
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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41 amplicon_info_file.close()
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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44 if __name__ == '__main__':
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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45 parser = argparse.ArgumentParser(description='Write an amplicon info file for iVar from a BED file describing primer positions')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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46 parser.add_argument('bed_file', type=argparse.FileType(), help='Primer BED file')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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47 parser.add_argument('amplicon_info_file', type=argparse.FileType('w'), help='Output file: amplicon info file in TSV format')
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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48 args = parser.parse_args()
aea7008fe1f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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50 write_amplicon_info_file(args.bed_file, args.amplicon_info_file)