Mercurial > repos > iuc > ivar_filtervariants
view write_amplicon_info_file.py @ 12:8f8df367470d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author | iuc |
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date | Mon, 13 Feb 2023 17:28:58 +0000 |
parents | 0135f1d487a0 |
children |
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#!/usr/bin/env python import argparse import re 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 = {} for line in bed_file: line = line.strip() if not line: continue fields = line.split('\t') start = int(fields[1]) name = fields[3] re_match = AMPLICON_PAT.match(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, start)) amplicon_sets[amplicon_id] = amplicon_set # 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' ) args = parser.parse_args() write_amplicon_info_file(args.bed_file, args.amplicon_info_file)