def test_unclassifiable_sequence(self):
query_file = StringIO(
">MostlyTs\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n")
res = mothur_classify_file(
query_file, self.ref_file.name, self.tax_file.name)
exp_res = {
'MostlyTs': (['Unknown'], 0.0),
}
self.assertEqual(res, exp_res)
def test_mothur_classify_file(self):
query_file = StringIO(mothur_seqs)
res = mothur_classify_file(
query_file, self.ref_file.name, self.tax_file.name)
exp_res = {
'A': (['k__Bacteria', 'p__Firmicutes', 'c__Clostridia',
'o__Clostridale', 'f__Eubacteriaceae', 'g__Eubacterium',
's__Eubacteriumfoedans'], 1.0),
'Very': (['k__Bacteria', 'p__Bacteriodetes'], 1.0),
'01': (['k__Bacteria', 'p__Firmicutes'], 1.0),
}
self.assertEqual(res, exp_res)
def __call__(self, seq_path, result_path=None, log_path=None):
seq_file = open(seq_path)
percent_confidence = int(self.Params['Confidence'] * 100)
result = mothur.mothur_classify_file(
query_file=seq_file,
ref_fp=self.Params['reference_sequences_fp'],
tax_fp=self.Params['id_to_taxonomy_fp'],
cutoff=percent_confidence,
iters=self.Params['Iterations'],
ksize=self.Params['KmerSize'],
output_fp=result_path,
)
if log_path:
self.writeLog(log_path)
return result
def __call__(self, seq_path, result_path=None, log_path=None):
seq_file = open(seq_path)
percent_confidence = int(self.Params['Confidence'] * 100)
result = mothur.mothur_classify_file(
query_file=seq_file,
ref_fp=self.Params['reference_sequences_fp'],
tax_fp=self.Params['id_to_taxonomy_fp'],
cutoff=percent_confidence,
iters=self.Params['Iterations'],
ksize=self.Params['KmerSize'],
output_fp=result_path,
)
if log_path:
self.writeLog(log_path)
return result