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)