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 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
)
)
class FastaTestCase(unittest.TestCase):
@classmethod
def setUp(self):
self.fasta = Fasta(testdata.PARSE_FASTA,
'test_fasta',
'test_aligner',
is_reference=False)
def test_repr(self):
expected = "Fasta(filepath='{0}', name='test_fasta', aligner='test_aligner', is_reference=False)".format(
testdata.PARSE_FASTA)
self.assertEqual(expected, repr(self.fasta))
def test_identifier(self):
expected = 'test_fasta::test_aligner'
self.assertEqual(expected, self.fasta.identifier)
def test_get_contig(self):
"""
The following tests assume FastaContig is working.
"""
# It should return the correct contig at any file position or in any order.
contig0 = self.fasta.get_contig('contig0')
contig2 = self.fasta.get_contig('contig2')
contig1 = self.fasta.get_contig('contig1')
self.assertEqual('contig0', contig0.name)
self.assertEqual('contig1', contig1.name)
self.assertEqual('contig2', contig2.name)
def test_get_contig_empty(self):
contig = self.fasta.get_contig('DoesNotExist')
self.assertIsInstance(contig, EmptyContig)
def test_yields_contigs_longest_to_shortest(self):
expected = [
'gi|129295|sp|P01013|OVAX_CHICK', '100CharacterContig',
'90CharacterContig', '90CharacterContigNoBreak',
'90CharacterContig2'
]
for contig, expect in zip(self.fasta.contigs, expected):
self.assertEqual(expect, contig.name)
class FastaTestCase(unittest.TestCase):
@classmethod
def setUp(self):
self.fasta = Fasta(testdata.PARSE_FASTA, 'test_fasta', 'test_aligner', is_reference=False)
def test_repr(self):
expected = "Fasta(filepath='{0}', name='test_fasta', aligner='test_aligner', is_reference=False)".format(
testdata.PARSE_FASTA)
self.assertEqual(expected, repr(self.fasta))
def test_identifier(self):
expected = 'test_fasta::test_aligner'
self.assertEqual(expected, self.fasta.identifier)
def test_get_contig(self):
"""
The following tests assume FastaContig is working.
"""
# It should return the correct contig at any file position or in any order.
contig0 = self.fasta.get_contig('contig0')
contig2 = self.fasta.get_contig('contig2')
contig1 = self.fasta.get_contig('contig1')
self.assertEqual('contig0', contig0.name)
self.assertEqual('contig1', contig1.name)
self.assertEqual('contig2', contig2.name)
def test_get_contig_empty(self):
contig = self.fasta.get_contig('DoesNotExist')
self.assertIsInstance(contig, EmptyContig)
def test_yields_contigs_longest_to_shortest(self):
expected = [
'gi|129295|sp|P01013|OVAX_CHICK',
'100CharacterContig',
'90CharacterContig',
'90CharacterContigNoBreak',
'90CharacterContig2'
]
for contig, expect in zip(self.fasta.contigs, expected):
self.assertEqual(expect, contig.name)
def setUp(self):
self.fasta = Fasta(testdata.PARSE_FASTA, 'test_fasta', 'test_aligner', is_reference=False)
def setUp(self):
self.fasta = Fasta(testdata.PARSE_FASTA,
'test_fasta',
'test_aligner',
is_reference=False)