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_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 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)
