def test_exclude_seqs_left_justify_value_error(self):
with self.assertRaisesRegex(ValueError, "left_justify is not "
"compatible with "
"method='blast'"):
exclude_seqs(
self.query_seqs_left_justify, self.bacterial_ref,
method=self.method, left_justify=True)
def test_exclude_seqs_all_miss(self):
obs, missed = exclude_seqs(
self.query_seqs_with_mismatch, self.fungal_ref, method=self.method)
self.assertEqual(sorted(missed.index), sorted(
_dnafastaformats_to_series(
self.query_seqs_with_mismatch).index))
self.assertEqual(sorted(obs.index), [])
def test_exclude_seqs_bacterial_hit_fungal_miss(self):
obs, missed = exclude_seqs(
self.query_seqs, self.bacterial_ref, method=self.method)
self.assertEqual(
sorted(obs.index), sorted(self.bacterial_exp.index))
self.assertEqual(
sorted(missed.index), sorted(self.fungal_exp.index))
def test_exclude_seqs_short_seqs_miss_with_blastn_short_low_eval(self):
obs, missed = obs, missed = exclude_seqs(
self.query_seqs_short, self.bacterial_ref,
method='blastn-short', perc_identity=0.01, evalue=10**-30)
self.assertEqual(sorted(missed.index), sorted(
_dnafastaformats_to_series(self.query_seqs_short).index))
self.assertEqual(sorted(obs.index), [])
def test_exclude_seqs_short_seqs_hit_with_blastn_short(self):
obs, missed = obs, missed = exclude_seqs(
self.query_seqs_short, self.bacterial_ref,
method='blastn-short', evalue=10000)
self.assertEqual(sorted(obs.index), sorted(
_dnafastaformats_to_series(self.query_seqs_short).index))
self.assertEqual(sorted(missed.index), [])
def test_exclude_seqs_96_perc_identity(self):
obs, missed = exclude_seqs(
self.query_seqs_with_mismatch, self.bacterial_ref,
method=self.method, perc_identity=0.965)
self.assertEqual(
sorted(obs.index), ['2MISA', '2MISB', '8MISA', '8MISB'])
self.assertEqual(
sorted(missed.index), ['10MISA'])
def test_exclude_seqs_high_evalue_low_perc_query_aligned_permissive(self):
obs, missed = exclude_seqs(
self.query_seqs_part_rand, self.bacterial_ref,
method='blast', perc_identity=0.97, evalue=10000000000000000,
perc_query_aligned=0.1)
self.assertEqual(sorted(obs.index), sorted(
_dnafastaformats_to_series(self.query_seqs_part_rand).index))
self.assertEqual(sorted(missed.index), [])
def test_exclude_seqs_99_perc_identity(self):
obs, missed = exclude_seqs(
self.query_seqs_with_mismatch, self.bacterial_ref,
method=self.method, perc_identity=0.99)
self.assertEqual(sorted(missed.index), sorted(
_dnafastaformats_to_series(
self.query_seqs_with_mismatch).index))
self.assertEqual(sorted(obs.index), [])
def test_exclude_seqs_all_hit(self):
obs, missed = exclude_seqs(self.query_seqs,
self.query_seqs,
method=self.method)
self.assertEqual(
sorted(obs.index),
sorted(_dnafastaformats_to_series(self.query_seqs).index))
self.assertEqual(sorted(missed.index), [])
def test_exclude_seqs_short_seqs_hit_with_default_vsearch(self):
obs, missed = exclude_seqs(self.query_seqs_short,
self.bacterial_ref,
method='vsearch')
self.assertEqual(
sorted(obs.index),
sorted(_dnafastaformats_to_series(self.query_seqs_short).index))
self.assertEqual(sorted(missed.index), [])
def test_exclude_seqs_blast_low_evalue_discards_weak_matches(self):
obs, missed = exclude_seqs(
self.query_seqs_part_rand, self.bacterial_ref,
method='blast', perc_identity=0.97, evalue=10**-30,
perc_query_aligned=0.1)
self.assertEqual(
sorted(obs.index), ['YAYIMATCH'])
self.assertEqual(
sorted(missed.index), ['RAND1', 'RAND2'])
def test_exclude_seqs_left_justify_hits(self):
obs, missed = exclude_seqs(
self.query_seqs_left_justify, self.bacterial_ref,
method=self.method,
left_justify=True)
self.assertCountEqual(
sorted(obs.index),
['1111886-leftjustmatch', '1111882-leftjustwithindel',
'1111879-leftjustmatch']
)
def test_exclude_seqs_left_justify_missed(self):
obs, missed = exclude_seqs(
self.query_seqs_left_justify, self.bacterial_ref,
method=self.method, left_justify=True)
self.assertEqual(sorted(missed.index), ['1111883-noleftjustmatch'])
