def test_directory_format_wrong_filename(self):
filepath = self.get_data_path('qiime1-demux-format/short.fna')
shutil.copy(filepath, self.temp_dir.name)
with self.assertRaisesRegex(ValidationError,
r'QIIME1DemuxDirFmt.*seqs\.fna'):
QIIME1DemuxDirFmt(self.temp_dir.name, mode='r').validate()
def test_directory_format_validate_negative(self):
for file in self.negatives:
filepath = self.get_data_path('qiime1-demux-format/%s' % file)
shutil.copy(filepath, os.path.join(self.temp_dir.name, 'seqs.fna'))
with self.assertRaisesRegex(ValidationError, 'QIIME1DemuxFormat'):
QIIME1DemuxDirFmt(self.temp_dir.name, mode='r').validate()
def test_dereplicate_sequences_prefix(self):
input_sequences_fp = self.get_data_path('seqs-1')
input_sequences = QIIME1DemuxDirFmt(input_sequences_fp, 'r')
exp_table = biom.Table(np.array([[2, 2],
[2, 0]]),
['4574b947a0159c0da35a1f30f989681a1d9f64ef',
'16a1263bde4f2f99422630d1bb87935c4236d1ba'],
['s2', 'sample1'])
with redirected_stdio(stderr=os.devnull):
obs_table, obs_sequences = dereplicate_sequences(
sequences=input_sequences, derep_prefix=True)
# order of identifiers is important for biom.Table equality
obs_table = \
obs_table.sort_order(exp_table.ids(axis='observation'),
axis='observation')
self.assertEqual(obs_table, exp_table)
# sequences are reverse-sorted by abundance in output
obs_seqs = list(skbio.io.read(str(obs_sequences),
constructor=skbio.DNA, format='fasta'))
exp_seqs = [skbio.DNA('AAACGTTACGGTTAACTATACATGCAGAAGACTAATCGG',
metadata={'id': ('4574b947a0159c0da35a1f30f'
'989681a1d9f64ef'),
'description': 's2_1'}),
skbio.DNA('ACGTACGTACGTACGTACGTACGTACGTACGTGCATGGTGCGACCG',
metadata={'id': ('16a1263bde4f2f99422630d1bb'
'87935c4236d1ba'),
'description': 's2_42'})]
self.assertEqual(obs_seqs, exp_seqs)
def test_directory_format_validate_positive(self):
for file in self.positives:
filepath = self.get_data_path('qiime1-demux-format/%s' % file)
shutil.copy(filepath, os.path.join(self.temp_dir.name, 'seqs.fna'))
QIIME1DemuxDirFmt(self.temp_dir.name, mode='r').validate()