def test_bad_values_fail(self):
# Just confirm that the machinery works, anything more specific is just
# restating the _valid_inputs dict which is more declarative than a
# unit-test anyways.
with self.assertRaisesRegex(ValueError, 'trim_length'):
denoise_other(self.demux_seqs, self.ref, -123)
with self.assertRaisesRegex(ValueError, 'min_reads'):
denoise_other(self.demux_seqs, self.ref, 100, min_reads=-1)
def test_defaults(self):
fp = self.get_data_path('expected/other-default.biom')
exp_tab = biom.load_table(fp)
exp_rep_seqs = list(
skbio.io.read(self.get_data_path('expected/other-default.fasta'),
'fasta',
constructor=skbio.DNA,
lowercase='ignore'))
for seq in exp_rep_seqs:
del seq.metadata['description']
obs_tab, rep_seqs, stats = denoise_other(self.demux_seqs, self.ref,
100)
rep_seqs = _sort_seqs(rep_seqs)
exp_rep_seqs = _sort_seqs(exp_rep_seqs)
self.assertEqual(rep_seqs, exp_rep_seqs)
self.assertEqual(obs_tab, exp_tab)
self.assertEqual(list(stats.columns), STATS_HEADER[1:])
self.assertEqual(len(stats), 0)
def test_all_reads_filtered(self):
with self.assertRaisesRegex(ValueError, 'filter'):
denoise_other(self.demux_seqs, self.ref, 10000)