Example #1
0
    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)
Example #2
0
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')