def test_uchime_denovo_no_chimeras(self):
input_table = biom.Table(
np.array([[3, 4, 2], [1, 0, 0], [4, 5, 6], [2, 2, 2]]),
['feature1', 'feature2', 'feature3', 'feature4'],
['sample1', 'sample2', 'sample3'])
with redirected_stdio(stderr=os.devnull):
chime, nonchime, stats = uchime_denovo(
sequences=self.input_sequences, table=input_table)
obs_chime = _read_seqs(chime)
exp_chime = []
self.assertEqual(obs_chime, exp_chime)
# sequences are reverse-sorted by abundance in output
obs_nonchime = _read_seqs(nonchime)
exp_nonchime = [
self.input_sequences_list[2], self.input_sequences_list[0],
self.input_sequences_list[3], self.input_sequences_list[1]
]
self.assertEqual(obs_nonchime, exp_nonchime)
with stats.open() as stats_fh:
stats_text = stats_fh.read()
self.assertTrue('feature1' in stats_text)
self.assertTrue('feature2' in stats_text)
self.assertTrue('feature3' in stats_text)
self.assertTrue('feature4' in stats_text)
stats_lines = [e for e in stats_text.split('\n') if len(e) > 0]
self.assertEqual(len(stats_lines), 4)
def test_uchime_denovo(self):
with redirected_stdio(stderr=os.devnull):
chime, nonchime, stats = uchime_denovo(
sequences=self.input_sequences, table=self.input_table)
obs_chime = _read_seqs(chime)
exp_chime = [self.input_sequences_list[3]]
self.assertEqual(obs_chime, exp_chime)
# sequences are reverse-sorted by abundance in output
obs_nonchime = _read_seqs(nonchime)
exp_nonchime = [
self.input_sequences_list[0], self.input_sequences_list[1],
self.input_sequences_list[2]
]
self.assertEqual(obs_nonchime, exp_nonchime)
with stats.open() as stats_fh:
stats_text = stats_fh.read()
self.assertTrue('feature1' in stats_text)
self.assertTrue('feature2' in stats_text)
self.assertTrue('feature3' in stats_text)
self.assertTrue('feature4' in stats_text)
stats_lines = [e for e in stats_text.split('\n') if len(e) > 0]
self.assertEqual(len(stats_lines), 4)