Mercurial > repos > iuc > ivar_variants
view prepare_amplicon_info.py @ 15:045d6d00f606 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
author | iuc |
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date | Tue, 27 Jun 2023 17:13:41 +0000 |
parents | 584beffa972b |
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#!/usr/bin/env python # extends ivar trim's amplicon info parsing abilities # to include calculation of amplicon regions from # sets of nested (more than two) primers import sys # parse primers and their start positions from BED file primer_starts = {} with open(sys.argv[1]) as i: for line in i: line = line.strip() if not line: continue f = line.split('\t') try: if f[5] == '+': primer_starts[f[3]] = int(f[1]) elif f[5] == '-': primer_starts[f[3]] = int(f[2]) - 1 else: raise ValueError() except (IndexError, ValueError): sys.exit( 'Primer BED file needs to be TAB-separated with the ' 'following columns: ' 'chrom, chromStart, chromEnd, name, score, strand, ' 'where "chromStart", "chromEnd" need to be integer values ' 'and "strand" needs to be either "+" or "-".' ) # parse amplicon info and record outer primer names with open(sys.argv[2]) as i: ret_lines = [] for line in i: line = line.strip() if not line: continue first = last = None for pname in line.split('\t'): try: primer_start = primer_starts[pname] except KeyError: sys.exit( 'Amplicon info with primer name not found in ' f'primer BED file: "{pname}"' ) if first is None or primer_start < primer_starts[first]: first = pname if last is None or primer_start > primer_starts[last]: last = pname if first == last: sys.exit( line + 'is not a proper amplicon info line.' ) ret_lines.append(f'{first}\t{last}\n') # write amended amplicon info with open(sys.argv[3], 'w') as o: o.writelines(ret_lines)