def test_defaults(self):
with open(self.get_data_path('expected/pyro-default.tsv')) as fh:
exp_table = biom.Table.from_tsv(fh, None, None, lambda x: x)
exp_rep_seqs = list(
skbio.io.read(self.get_data_path('expected/pyro-default.fasta'),
'fasta',
constructor=skbio.DNA))
for seq in exp_rep_seqs:
del seq.metadata['description']
exp_md = qiime2.Metadata.load(
self.get_data_path('expected/pyro-default-stats.tsv'))
table, rep_seqs, md = denoise_pyro(self.demux_seqs, 100)
self.assertEqual(table, exp_table)
self.assertEqual(_sort_seqs(rep_seqs), _sort_seqs(exp_rep_seqs))
self.assertEqual(md, exp_md)
def test_trunc_len_bigger_than_max_len(self):
with self.assertRaisesRegex(ValueError, 'max_len'):
denoise_pyro(self.demux_seqs, 100, max_len=99)
# Shouldn't fail when max_len > trunc_len
denoise_pyro(self.demux_seqs, 100, max_len=160)