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Readability improvements.
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@andrewsanchez
andrewsanchez committed Nov 19, 2020
1 parent f6adcb5 commit 130ad2e
Showing 1 changed file with 77 additions and 40 deletions.
117 changes: 77 additions & 40 deletions q2_cutadapt/tests/test_demux.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def assert_demux_results(self, exp_samples_and_barcodes, exp_results,
self.assertTrue(sample_id in filename)
self.assertTrue(barcode in filename)
with gzip.open(str(fmt), 'rt') as fh:
obs = fh.readlines()
obs = ''.join(fh.readlines())
self.assertEqual(exp, obs)

def assert_untrimmed_results(self, exp, obs_untrimmed_art):
Expand All @@ -68,11 +68,15 @@ def test_typical(self):
metadata = CategoricalMetadataColumn(
pd.Series(['AAAA', 'CCCC'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b'], name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -87,12 +91,17 @@ def test_all_matched(self):
pd.Series(['AAAA', 'CCCC', 'GGGG'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b', 'sample_c'],
name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id6\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n',
# sample c
'@id6\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -118,6 +127,11 @@ def test_error_tolerance_filtering(self):
exp = [['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -136,11 +150,15 @@ def test_error_tolerance_high_enough_to_prevent_filtering(self):
metadata = CategoricalMetadataColumn(
pd.Series(['AAAG', 'CCCC'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b'], name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -157,12 +175,17 @@ def test_extra_barcode_in_metadata(self):
pd.Series(['AAAA', 'CCCC', 'GGGG', 'TTTT'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b', 'sample_c',
'sample_d'], name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id6\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n',
# sample c
'@id6\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -186,12 +209,17 @@ def test_variable_length_barcodes(self):
muxed_sequences_fp = self.get_data_path('variable_length.fastq.gz')
muxed_sequences = Artifact.import_data(
'MultiplexedSingleEndBarcodeInSequence', muxed_sequences_fp)
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id6\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n',
# sample c
'@id6\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -204,11 +232,15 @@ def test_batch_size(self):
metadata = CategoricalMetadataColumn(
pd.Series(['AAAA', 'CCCC'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b'], name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
Expand All @@ -232,12 +264,17 @@ def test_batch_size_odd_number_of_samples(self):
pd.Series(['AAAA', 'CCCC', 'GGGG'], name='Barcode',
index=pd.Index(['sample_a', 'sample_b', 'sample_c'],
name='id')))
exp = [['@id1\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id3\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id2\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id4\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n',
'@id5\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n'],
['@id6\n', 'ACGTACGT\n', '+\n', 'zzzzzzzz\n']]
exp = [
# sample a
'@id1\nACGTACGT\n+\nzzzzzzzz\n'
'@id3\nACGTACGT\n+\nzzzzzzzz\n',
# sample b
'@id2\nACGTACGT\n+\nzzzzzzzz\n'
'@id4\nACGTACGT\n+\nzzzzzzzz\n'
'@id5\nACGTACGT\n+\nzzzzzzzz\n',
# sample c
'@id6\nACGTACGT\n+\nzzzzzzzz\n'
]

with redirected_stdio(stderr=os.devnull):
obs_demuxed_art, obs_untrimmed_art = \
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