def test_summarize_taxonomic_agreement_multiple_otus(self):
"""Test writing out the taxonomic agreement for multiple OTUs."""
exp = [
'A\t2\t\'1\',\'2\'\t100.00%\t100.00%\t50.00%\tA\tB\tC,D\n',
'B\t1\t\'3\'\t100.00%\t100.00%\t100.00%\tA\tZ\tT\n'
]
obs = summarize_taxonomic_agreement(self.otu_map2, self.tax_map1, 3)
self.assertEqual(obs, exp)
def test_summarize_taxonomic_agreement_standard(self):
"""Test writing out the taxonomic agreement for seqs in OTUs."""
exp = [
'A\t3\t\'1\',\'2\',\'3\'\t100.00%\t66.67%\t33.33%\tA\tB,Z\t'
'C,D,T\n'
]
obs = summarize_taxonomic_agreement(self.otu_map1, self.tax_map1, 3)
self.assertEqual(obs, exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
results = summarize_taxonomic_agreement(
open(opts.otu_map_fp, 'U').readlines(),
open(opts.input_taxonomy_map, 'U').readlines())
out_f = open(opts.output_fp, 'w')
out_f.write('OTU_ID\tSize\tSeq_IDs\tDomain\tKingdom\tPhylum\tClass\t'
'Order\tFamily\tGenus\tSpecies\tDomain\tKingdom\tPhylum\t'
'Class\tOrder\tFamily\tGenus\tSpecies\n')
for line in results:
out_f.write(line)
out_f.close()
def test_summarize_taxonomic_agreement_multiple_otus(self):
"""Test writing out the taxonomic agreement for multiple OTUs."""
exp = ['A\t2\t\'1\',\'2\'\t100.00%\t100.00%\t50.00%\tA\tB\tC,D\n',
'B\t1\t\'3\'\t100.00%\t100.00%\t100.00%\tA\tZ\tT\n']
obs = summarize_taxonomic_agreement(self.otu_map2, self.tax_map1, 3)
self.assertEqual(obs, exp)
def test_summarize_taxonomic_agreement_standard(self):
"""Test writing out the taxonomic agreement for seqs in OTUs."""
exp = ['A\t3\t\'1\',\'2\',\'3\'\t100.00%\t66.67%\t33.33%\tA\tB,Z\t'
'C,D,T\n']
obs = summarize_taxonomic_agreement(self.otu_map1, self.tax_map1, 3)
self.assertEqual(obs, exp)
