Mercurial > repos > iuc > ivar_filtervariants

annotate write_amplicon_info_file.py @ 9:47a27906d750 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
author iuc
date Fri, 20 Aug 2021 20:32:33 +0000
parents b93845a04cc8
children 0135f1d487a0
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1 #!/usr/bin/env python
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3 import argparse
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4 import re
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7 AMPLICON_PAT = re.compile(r'.*_(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)')
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10 def write_amplicon_info_file(bed_file, amplicon_info_file):
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11 amplicon_sets = {}
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12 for line in bed_file:
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13 fields = line.strip().split('\t')
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14 start = int(fields[1])
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15 name = fields[3]
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16 re_match = AMPLICON_PAT.match(name)
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17 if re_match is None:
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18 raise ValueError(
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19 '{} does not match expected amplicon name format'.format(name)
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20 )
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21 amplicon_id = int(re_match.group('num'))
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22 amplicon_set = amplicon_sets.get(amplicon_id, [])
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23 amplicon_set.append((name, start))
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24 amplicon_sets[amplicon_id] = amplicon_set
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25
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26 # write amplicons sorted by number with primers sorted by start position
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27 for id in sorted(amplicon_sets):
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28 amplicon_info = '\t'.join(
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29 [name for name, start in sorted(
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30 amplicon_sets[id], key=lambda x: x[1]
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31 )]
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32 ) + '\n'
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33 amplicon_info_file.write(amplicon_info)
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34 amplicon_info_file.close()
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37 if __name__ == '__main__':
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38 parser = argparse.ArgumentParser(
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39 description='Write an amplicon info file for iVar '
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40 'from a BED file describing primer positions'
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41 )
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42 parser.add_argument(
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43 'bed_file', type=argparse.FileType(), help='Primer BED file'
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44 )
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45 parser.add_argument(
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46 'amplicon_info_file', type=argparse.FileType('w'),
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47 help='Output file: amplicon info file in TSV format'
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48 )
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49 args = parser.parse_args()
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51 write_amplicon_info_file(args.bed_file, args.amplicon_info_file)