| Previous changeset 8:aea7008fe1f1 (2021-08-05) Next changeset 10:584beffa972b (2022-07-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7" |
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modified:
write_amplicon_info_file.py |
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| diff -r aea7008fe1f1 -r 3888bbe7a9ca write_amplicon_info_file.py --- a/write_amplicon_info_file.py Thu Aug 05 12:44:05 2021 +0000 +++ b/write_amplicon_info_file.py Fri Aug 20 20:33:21 2021 +0000 |
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| @@ -3,48 +3,49 @@ import argparse import re -AMPLICON_NAME_RE = r'.*_(?P<num>\d+)_[^0-9]*(?P<name>L(?:EFT)?|R(?:IGHT)?)' - -def primer_info_to_position(name): - position = 0 - re_match = re.match(AMPLICON_NAME_RE, name) - if re_match is None: - raise ValueError("{} does not match expected amplicon name format".format(name)) - side = re_match.group('name') - num = re_match.group('num') - if side == 'RIGHT' or side == 'R': - position += 1000 - if num is not None: - position += int(num) - return position +AMPLICON_PAT = re.compile(r'.*_(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)') def write_amplicon_info_file(bed_file, amplicon_info_file): amplicon_sets = {} - amplicon_ids = set() for line in bed_file: fields = line.strip().split('\t') + start = int(fields[1]) name = fields[3] - re_match = re.match(AMPLICON_NAME_RE, name) + re_match = AMPLICON_PAT.match(name) if re_match is None: - raise ValueError("{} does not match expected amplicon name format".format(name)) + raise ValueError( + '{} does not match expected amplicon name format'.format(name) + ) amplicon_id = int(re_match.group('num')) amplicon_set = amplicon_sets.get(amplicon_id, []) - amplicon_set.append(name) + amplicon_set.append((name, start)) amplicon_sets[amplicon_id] = amplicon_set - amplicon_ids.add(amplicon_id) - for id in sorted(list(amplicon_ids)): - amplicon_info = '\t'.join([name for name in sorted(amplicon_sets[id], key=primer_info_to_position)]) + '\n' + # write amplicons sorted by number with primers sorted by start position + for id in sorted(amplicon_sets): + amplicon_info = '\t'.join( + [name for name, start in sorted( + amplicon_sets[id], key=lambda x: x[1] + )] + ) + '\n' amplicon_info_file.write(amplicon_info) amplicon_info_file.close() if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Write an amplicon info file for iVar from a BED file describing primer positions') - parser.add_argument('bed_file', type=argparse.FileType(), help='Primer BED file') - parser.add_argument('amplicon_info_file', type=argparse.FileType('w'), help='Output file: amplicon info file in TSV format') + parser = argparse.ArgumentParser( + description='Write an amplicon info file for iVar ' + 'from a BED file describing primer positions' + ) + parser.add_argument( + 'bed_file', type=argparse.FileType(), help='Primer BED file' + ) + parser.add_argument( + 'amplicon_info_file', type=argparse.FileType('w'), + help='Output file: amplicon info file in TSV format' + ) args = parser.parse_args() write_amplicon_info_file(args.bed_file, args.amplicon_info_file) |