def test_parse_uchime_chimeras(self): """Parse uchime chimera output""" inlines = ["1.7308 GU234509.1 94_12740_108965 94_6884_155789 99.6 98.0 95.5 93.9 98.0 51 1 3 22 2 2 1.63 Y\n", "0.0000 HQ316978.1 * * * * * * * * * * * * * * N\n", "0.0190 HQ316968.1 94_6884_155789 94_28256_783727 97.8 97.5 97.4 99.3 97.5 6 0 18 4 3 8 0.33 N\n"] exp = [('GU234509.1', 1.7308, '94_12740_108965','94_6884_155789')] obs = parse_uchime_chimeras(inlines) self.assertEqual(obs, exp)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) taxlookup = load_consensus_map(open(opts.ref_taxonomy_map)) uchime_results = parse_uchime_chimeras(open(opts.input_uchime)) output = open(opts.output, 'w') output.write("#accession\treason\tnote\tnote\n") for id_, score, parent_a, parent_b in uchime_results: if determine_taxon_conflict(taxlookup, parent_a, parent_b): o = [id_, "Class conflict found by UCHIME"] o.append("%s: %s" % (parent_a, '; '.join(taxlookup[parent_a]))) o.append("%s: %s" % (parent_b, '; '.join(taxlookup[parent_b]))) output.write('\t'.join(o)) output.write('\n')
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) taxlookup = load_consensus_map(open(opts.ref_taxonomy_map)) uchime_results = parse_uchime_chimeras(open(opts.input_uchime)) output = open(opts.output,'w') output.write("#accession\treason\tnote\tnote\n") for id_, score, parent_a, parent_b in uchime_results: if determine_taxon_conflict(taxlookup, parent_a, parent_b): o = [id_,"Class conflict found by UCHIME"] o.append("%s: %s" % (parent_a, '; '.join(taxlookup[parent_a]))) o.append("%s: %s" % (parent_b, '; '.join(taxlookup[parent_b]))) output.write('\t'.join(o)) output.write('\n')