| Previous changeset 7:4abcfbc2e5b6 (2021-06-11) Next changeset 9:47a27906d750 (2021-08-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d" |
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added:
write_amplicon_info_file.py |
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| diff -r 4abcfbc2e5b6 -r b93845a04cc8 write_amplicon_info_file.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_amplicon_info_file.py Thu Aug 05 12:43:17 2021 +0000 |
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| @@ -0,0 +1,50 @@ +#!/usr/bin/env python + +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 + + +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') + name = fields[3] + re_match = re.match(AMPLICON_NAME_RE, name) + if re_match is None: + 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_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' + 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') + args = parser.parse_args() + + write_amplicon_info_file(args.bed_file, args.amplicon_info_file) |