def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
taxlookup = load_consensus_map(open(opts.ref_taxonomy_map), False)
cs_results = parse_cs_chimeras(open(opts.input_cs))
b3_results = parse_b3_chimeras(open(opts.input_bellerophon))
output = open(opts.output, 'w')
output.write("#accession\treason\tnote\tnote\n")
overlap = get_overlap(b3_results, cs_results)
for id_ in overlap:
output.write("%s\tFound by both Bellerophon and ChimeraSlayer\n" % id_)
for id_, score, parent_a, parent_b in b3_results:
if id_ in overlap:
continue
if determine_taxon_conflict(taxlookup, parent_a, parent_b):
o = [id_, "Class conflict found by Bellerophon"]
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')
for id_, parent_a, parent_b in cs_results:
if id_ in overlap:
continue
if determine_taxon_conflict(taxlookup, parent_a, parent_b):
o = [id_, "Class conflict found by ChimeraSlayer"]
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), False)
cs_results = parse_cs_chimeras(open(opts.input_cs))
b3_results = parse_b3_chimeras(open(opts.input_bellerophon))
output = open(opts.output,'w')
output.write("#accession\treason\tnote\tnote\n")
overlap = get_overlap(b3_results, cs_results)
for id_ in overlap:
output.write("%s\tFound by both Bellerophon and ChimeraSlayer\n" % id_)
for id_, score, parent_a, parent_b in b3_results:
if id_ in overlap:
continue
if determine_taxon_conflict(taxlookup, parent_a, parent_b):
o = [id_,"Class conflict found by Bellerophon"]
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')
for id_, parent_a, parent_b in cs_results:
if id_ in overlap:
continue
if determine_taxon_conflict(taxlookup, parent_a, parent_b):
o = [id_,"Class conflict found by ChimeraSlayer"]
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 test_parse_cs_chimeras(self):
"""Parse ChimeraSlayer output"""
inlines = ["a\tparentfoo\tparentbar\n",
"123x\txyz\tabc\n"]
exp = [('a','parentfoo','parentbar'),
('123x','xyz','abc')]
obs = parse_cs_chimeras(inlines)
self.assertEqual(obs,exp)