Beispiel #1
0
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_determine_taxon_conflict(self):
     """determine if there is a taxon conflict"""
     taxmap = {1:['a','b','c','d','e','f','g'],
               2:['a','b','c','d','e','f','x'],
               3:['a','b','z','q','w','t','y']}
     self.assertFalse(determine_taxon_conflict(taxmap, 1,2))
     self.assertTrue(determine_taxon_conflict(taxmap, 1,3))
Beispiel #3
0
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_determine_taxon_conflict(self):
     """determine if there is a taxon conflict"""
     taxmap = {
         1: ['a', 'b', 'c', 'd', 'e', 'f', 'g'],
         2: ['a', 'b', 'c', 'd', 'e', 'f', 'x'],
         3: ['a', 'b', 'z', 'q', 'w', 't', 'y']
     }
     self.assertFalse(determine_taxon_conflict(taxmap, 1, 2))
     self.assertTrue(determine_taxon_conflict(taxmap, 1, 3))
Beispiel #5
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')