def setUp(self):
fasta = Fasta(testdata.PARSE_FASTA, 'test_data', None, False)
ref_fasta = Fasta(testdata.PARSE_FASTA, 'test_data', None, True)
self.analysis = GenomeAnalysis(10, .9)
self.coroutine_fn = lambda *arg: (self.CoroutineMock(),
self.CoroutineMock())
self.dups_contig = fasta
self.reference_contig = ref_fasta.get_contig(
'ContigWithFilePositionOffset')
self.sample_groups = ((fasta, fasta), (fasta, ), (fasta, fasta))
def test_sample_analysis(self):
with TemporaryDirectory() as tmpdir:
matrix_dir = os.path.join(tmpdir, 'matrices')
stats_dir = os.path.join(tmpdir, 'statistics')
os.mkdir(matrix_dir)
os.mkdir(stats_dir)
genome_analysis = GenomeAnalysis(10, .9)
reference_fasta = Fasta(testdata.REFERENCE_FASTA, 'reference', 'aligner', is_reference=True)
reference_dups = Fasta(testdata.REFERENCE_DUPS, 'dups', 'aligner', is_reference=True)
write_matrix.analyze_samples(matrix_dir, stats_dir, genome_analysis, reference_fasta, reference_dups, sample_groups, max_workers=1)
def setUpClass(cls):
cls.analysis = GenomeAnalysis(10, 0.9)
def setUp(self):
self.analysis = GenomeAnalysis(10, 0.9)
def setUp(self):
vcf = StringIO(initial_value='')
fasta = StringIO(initial_value='')
self.analysis = GenomeAnalysis(10, 0.9)
