def test_w_sample_metadata(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table, metadata)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,4' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,1' in open(sample_freq_fp).read())
interactive_sample_detail_fp = \
os.path.join(output_dir, 'data.jsonp')
self.assertTrue(os.path.exists(interactive_sample_detail_fp))
self.assertTrue('SampleType' in
open(interactive_sample_detail_fp).read())
def test_basic(self):
table = biom.Table(np.array([[0, 1, 3],
[1, 1, 2],
[400, 450, 500],
[1000, 10000, 100000],
[52, 42, 99]]),
['O1', 'O2', '03', '04', 'O5'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,4' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,1453' in open(sample_freq_fp).read())
interactive_sample_detail_fp = \
os.path.join(output_dir, 'data.jsonp')
self.assertTrue(os.path.exists(interactive_sample_detail_fp))
def test_basic(self):
table = biom.Table(np.array([[0, 1, 3],
[1, 1, 2],
[400, 450, 500],
[1000, 10000, 100000],
[52, 42, 99]]),
['O1', 'O2', '03', '04', 'O5'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,4' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,1453' in open(sample_freq_fp).read())
interactive_sample_detail_fp = \
os.path.join(output_dir, 'data.jsonp')
self.assertTrue(os.path.exists(interactive_sample_detail_fp))
def test_w_sample_metadata(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table, metadata)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,4' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,1' in open(sample_freq_fp).read())
interactive_sample_detail_fp = \
os.path.join(output_dir, 'data.jsonp')
self.assertTrue(os.path.exists(interactive_sample_detail_fp))
self.assertTrue('SampleType' in
open(interactive_sample_detail_fp).read())
def test_one_sample(self):
sample_frequencies_pdf_fn = 'sample-frequencies.pdf'
# sample-frequencies.pdf should not be written when there is only
# one sample...
table = biom.Table(np.array([[0], [1]]), ['O1', 'O2'], ['S1'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
sample_frequencies_pdf_fp = \
os.path.join(output_dir, sample_frequencies_pdf_fn)
self.assertFalse(os.path.exists(sample_frequencies_pdf_fp))
# but it should be written when there is more than one sample
table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]), ['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
sample_frequencies_pdf_fp = \
os.path.join(output_dir, sample_frequencies_pdf_fn)
self.assertTrue(os.path.exists(sample_frequencies_pdf_fp))
def test_frequency_ranges_are_zero(self):
table = biom.Table(np.array([[25, 25, 25], [25, 25, 25]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,75' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,50' in open(sample_freq_fp).read())
def test_one_sample(self):
sample_frequencies_pdf_fn = 'sample-frequencies.pdf'
# sample-frequencies.pdf should not be written when there is only
# one sample...
table = biom.Table(np.array([[0], [1]]),
['O1', 'O2'],
['S1'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
sample_frequencies_pdf_fp = \
os.path.join(output_dir, sample_frequencies_pdf_fn)
self.assertFalse(os.path.exists(sample_frequencies_pdf_fp))
# but it should be written when there is more than one sample
table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
sample_frequencies_pdf_fp = \
os.path.join(output_dir, sample_frequencies_pdf_fn)
self.assertTrue(os.path.exists(sample_frequencies_pdf_fp))
def test_frequency_ranges_are_zero(self):
table = biom.Table(np.array([[25, 25, 25], [25, 25, 25]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, table)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
feature_freq_fp = os.path.join(output_dir,
'feature-frequency-detail.csv')
self.assertTrue(os.path.exists(feature_freq_fp))
self.assertTrue('O1,75' in open(feature_freq_fp).read())
sample_freq_fp = os.path.join(output_dir,
'sample-frequency-detail.csv')
self.assertTrue(os.path.exists(sample_freq_fp))
self.assertTrue('S1,50' in open(sample_freq_fp).read())
interactive_sample_detail_fp = \
os.path.join(output_dir, 'data.jsonp')
self.assertTrue(os.path.exists(interactive_sample_detail_fp))
