def test__index_contig_sorts_samples_by_identifier(self):
expected = (
'a::b',
'a::b,c',
'a::c',
'a::c,b',
'b::a',
'b::a,c',
'b::c',
'b::c,a',
'c::a',
'c::a,b',
'c::b',
'c::b,a'
)
(reference, dups, sample_groups) = vtm._index_contigs(
testdata.REFERENCE_FASTA,
testdata.REFERENCE_DUPS,
self.frankenfastas,
self.vcfs
)
for expect, observe in itertools.zip_longest(expected, itertools.chain.from_iterable(sample_groups)):
self.assertEqual(expect, observe.identifier)
def test__index_contig_sorts_samples_by_identifier(self):
expected = ('a::b', 'a::b,c', 'a::c', 'a::c,b', 'b::a', 'b::a,c',
'b::c', 'b::c,a', 'c::a', 'c::a,b', 'c::b', 'c::b,a')
(reference, dups,
sample_groups) = vtm._index_contigs(testdata.REFERENCE_FASTA,
testdata.REFERENCE_DUPS,
self.frankenfastas, self.vcfs)
for expect, observe in itertools.zip_longest(
expected, itertools.chain.from_iterable(sample_groups)):
self.assertEqual(expect, observe.identifier)
def test__index_contig(self):
(reference, dups,
sample_groups) = vtm._index_contigs(testdata.REFERENCE_FASTA,
testdata.REFERENCE_DUPS,
self.frankenfastas, self.vcfs)
self.assertIsInstance(reference, Fasta)
self.assertIsInstance(dups, Fasta)
# The individual sample analyses should be grouped by sample name; in this case a, b, and c
# In this test, each sample should have 4 analyses
for expected_sample_name, sample in zip(('a', 'b', 'c'),
sample_groups):
self.assertEqual(4, len(sample))
for analysis in sample:
self.assertEqual(expected_sample_name, analysis.name)
def test__index_contig(self):
(reference, dups, sample_groups) = vtm._index_contigs(
testdata.REFERENCE_FASTA,
testdata.REFERENCE_DUPS,
self.frankenfastas,
self.vcfs
)
self.assertIsInstance(reference, Fasta)
self.assertIsInstance(dups, Fasta)
# The individual sample analyses should be grouped by sample name; in this case a, b, and c
# In this test, each sample should have 4 analyses
for expected_sample_name, sample in zip(('a', 'b', 'c'), sample_groups):
self.assertEqual(4, len(sample))
for analysis in sample:
self.assertEqual(expected_sample_name, analysis.name)
