def test_descriptive_stats_integration(self):
seqs = DNAIterator(skbio.DNA(a, metadata=b)for a, b in (
('A', {'id': 'seq01'}),
('AA', {'id': 'seq02'}),
('AAA', {'id': 'seq03'}),
('AAAA', {'id': 'seq04'}),
('AAAA', {'id': 'seq05'}),
('AAA', {'id': 'seq06'}),
('AA', {'id': 'seq07'}),
('AAAAAAAAAA', {'id': 'seq08'})))
with tempfile.TemporaryDirectory() as output_dir:
tabulate_seqs(output_dir, seqs)
expected_fp = os.path.join(output_dir, 'index.html')
# all expected values are unique. If they all render in index.html, our
# function likely worked as expected.
with open(expected_fp) as fh:
file_text = fh.read()
self.assertTrue('<td>8</td>' in file_text)
self.assertTrue('<td>1</td>' in file_text)
self.assertTrue('<td>10</td>' in file_text)
self.assertTrue('<td>3.62</td>' in file_text)
self.assertTrue('<td>9</td>' in file_text)
self.assertTrue('<td>1</td>' in file_text)
self.assertTrue('<td>1</td>' in file_text)
self.assertTrue('<td>2</td>' in file_text)
self.assertTrue('<td>3</td>' in file_text)
self.assertTrue('<td>4</td>' in file_text)
self.assertTrue('<td>6</td>' in file_text)
self.assertTrue('<td>9</td>' in file_text)
def test_tsv_builder(self):
seqs = DNAIterator(
skbio.DNA(a, metadata=b) for a, b in (('A', {
'id': 'seq01'
}), ('AA', {
'id': 'seq02'
}), ('AAA', {
'id': 'seq03'
}), ('AAAA', {
'id': 'seq04'
}), ('AAAA', {
'id': 'seq05'
}), ('AAA', {
'id': 'seq06'
}), ('AA', {
'id': 'seq07'
}), ('AAAAAAAAAA', {
'id': 'seq08'
})))
# Do the files exist?
with tempfile.TemporaryDirectory() as output_dir:
tabulate_seqs(output_dir, seqs)
expected_stats_fp = os.path.join(output_dir,
'descriptive_stats.tsv')
expected_summary_fp = os.path.join(output_dir,
'seven_number_summary.tsv')
self.assertTrue(os.path.exists(expected_stats_fp))
self.assertTrue(os.path.exists(expected_summary_fp))
# Was data written to the files?
with open(expected_stats_fp) as stats_tsv:
tsv_reader = csv.reader(stats_tsv, dialect="excel-tab")
tsv_text = []
for row in tsv_reader:
tsv_text.append(row)
self.assertEqual(['Statistic', 'Value'], tsv_text[0])
self.assertEqual(['count', '8'], tsv_text[1])
with open(expected_summary_fp) as summ_tsv:
tsv_reader = csv.reader(summ_tsv, dialect="excel-tab")
tsv_text = []
for row in tsv_reader:
tsv_text.append(row)
self.assertEqual(['Quantile', 'Value'], tsv_text[0])
self.assertEqual(['0.02', '1.14'], tsv_text[1])
# Does link html generate correctly?
expected_index_fp = os.path.join(output_dir, 'index.html')
with open(expected_index_fp) as fh:
self.assertTrue('href="descriptive_stats.tsv"' in fh.read())
with open(expected_index_fp) as fh:
self.assertTrue('href="seven_number_summary.tsv"' in fh.read())
def test_basic(self):
seqs = DNAIterator(
(s for s in (skbio.DNA('ACGT', metadata={'id': 'seq1'}),
skbio.DNA('AAAA', metadata={'id': 'seq2'}))))
with tempfile.TemporaryDirectory() as output_dir:
tabulate_seqs(output_dir, seqs)
expected_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(expected_fp))
self.assertTrue('ACGT</a>' in open(expected_fp).read())
self.assertTrue('<td>seq2</td>' in open(expected_fp).read())
def test_basic(self):
seqs = DNAIterator(
(s for s in (skbio.DNA('ACGT', metadata={'id': 'seq1'}),
skbio.DNA('AAAA', metadata={'id': 'seq2'}))))
with tempfile.TemporaryDirectory() as output_dir:
tabulate_seqs(output_dir, seqs)
expected_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(expected_fp))
self.assertTrue('ACGT</a>' in open(expected_fp).read())
self.assertTrue('<td>seq2</td>' in open(expected_fp).read())
def test_basic(self):
seqs = DNAIterator(skbio.DNA(a, metadata=b) for a, b in(
('ACGT', {'id': 'seq1'}),
('AAAA', {'id': 'seq2'})))
with tempfile.TemporaryDirectory() as output_dir:
tabulate_seqs(output_dir, seqs)
expected_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(expected_fp))
with open(expected_fp) as fh:
file_text = fh.read()
self.assertTrue('ACGT</a>' in file_text)
self.assertTrue('<td>4</td>' in file_text)
self.assertTrue('<td>seq2</td>' in file_text)