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 SamplePositionsTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
def setUp(self):
vcf = StringIO(initial_value='')
fasta = StringIO(initial_value='')
self.analysis = GenomeAnalysis(10, 0.9)
def tearDown(self):
pass
@unittest.skip('Not Implemented')
def test_foo(self):
self.analysis.sample_positions('test_contig', self.sample_groups)
class SamplePositionsTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
def setUp(self):
vcf = StringIO(initial_value='')
fasta = StringIO(initial_value='')
self.analysis = GenomeAnalysis(10, 0.9)
def tearDown(self):
pass
@unittest.skip('Not Implemented')
def test_foo(self):
self.analysis.sample_positions('test_contig', self.sample_groups)
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 AnalyzeContigTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
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 tearDown(self):
pass
# def test_it_calls_the_coroutine_function_once(self):
# coroutine_fn_call_count = 0
#
# def coroutine_fn():
# return lambda *args: coroutine_fn_call_count += 1
#
# self.analysis.analyze_contig(coroutine_fn, sample_groups, dups_contig, reference_contig)
class CoroutineMock:
def send(self, arg):
pass
def test_it_collects_analysis_and_overall_contig_stats(self):
expected_analysis_stats = [
[
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}),
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0})
],
[
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}), Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}), Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}), Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0})
], [
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}), Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}), Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0})
], [
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}),
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}),
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0}),
Counter(
{'quality_breadth': 8, 'passed_proportion_filter': 8, 'called_reference': 8, 'was_called': 8,
'passed_coverage_filter': 8, 'called_snp': 0, 'called_degen': 0})
]
]
expected_contig_stats = Counter(
{'reference_clean': 8, 'all_passed_proportion': 8, 'quality_breadth': 8,
'Contig': 'ContigWithFilePositionOffset', 'reference_length': 8, 'best_snps': 0,
'all_passed_coverage': 8, 'reference_duplicated': 0, 'all_passed_consensus': 8, 'all_called': 8,
'any_snps': 0}
)
observed_analysis_stats, observed_contig_stats = self.analysis.analyze_contig(self.coroutine_fn,
self.sample_groups,
self.dups_contig,
self.reference_contig)
self.assertEqual(expected_analysis_stats, observed_analysis_stats)
self.assertEqual(expected_contig_stats, observed_contig_stats)
def setUp(self):
self.analysis = GenomeAnalysis(10, 0.9)
class AnalyzePositionTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
def setUp(self):
self.analysis = GenomeAnalysis(10, 0.9)
def tearDown(self):
pass
@unittest.skip('Not Implemented')
def test_it_filters_position_by_coverage(self):
"""
Change the coverage to check for a hardcoded value.
"""
self.analysis.analyze_position((), (), ())
@unittest.skip('Not Implemented')
def test_it_filters_position_by_proportion(self):
# Change the proportion to check for a hardcoded value.
self.analysis.analyze_position((), (), ())
def test_fasta_position(self):
reference_position = Position(
call='G',
coverage='-',
proportion='-'
)
dups_position = Position(
call='0',
coverage='-',
proportion='-'
)
samples = (
(
Position(
call='G',
coverage='-',
proportion='-'
),
Position(
call='G',
coverage='-',
proportion='-'
)
),
)
expected = PositionInfo(
is_all_called=True,
is_reference_clean=True,
is_reference_duplicated=False,
is_all_passed_coverage=True,
is_all_passed_proportion=True,
is_all_passed_consensus=True,
is_all_quality_breadth=True,
is_best_snp=False,
all_sample_stats=[
[
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0}),
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0})
], [
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0}),
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0}),
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0}),
Counter({'called_reference': 1, 'passed_coverage_filter': 1, 'quality_breadth': 1, 'was_called': 1,
'passed_proportion_filter': 1, 'called_snp': 0, 'called_degen': 0})
]
],
is_missing_matrix=False,
called_reference=2,
called_snp=0,
passed_coverage_filter=2,
passed_proportion_filter=2,
num_A=0,
num_C=0,
num_G=2,
num_T=0,
num_N=0,
call_str=['G', 'G', 'G'],
masked_call_str=['G', 'G', 'G'],
CallWasMade='YY',
PassedDepthFilter='--',
PassedProportionFilter='--',
Pattern=['1', '1', '1']
)
self.assertEqual(expected, self.analysis.analyze_position(reference_position, dups_position, samples))
def setUp(self):
vcf = StringIO(initial_value='')
fasta = StringIO(initial_value='')
self.analysis = GenomeAnalysis(10, 0.9)
class AnalyzeContigTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
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 tearDown(self):
pass
# def test_it_calls_the_coroutine_function_once(self):
# coroutine_fn_call_count = 0
#
# def coroutine_fn():
# return lambda *args: coroutine_fn_call_count += 1
#
# self.analysis.analyze_contig(coroutine_fn, sample_groups, dups_contig, reference_contig)
class CoroutineMock:
def send(self, arg):
pass
def test_it_collects_analysis_and_overall_contig_stats(self):
expected_analysis_stats = [[
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
})
],
[
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
})
],
[
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
})
],
[
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'quality_breadth': 8,
'passed_proportion_filter': 8,
'called_reference': 8,
'was_called': 8,
'passed_coverage_filter': 8,
'called_snp': 0,
'called_degen': 0
})
]]
expected_contig_stats = Counter({
'reference_clean': 8,
'all_passed_proportion': 8,
'quality_breadth': 8,
'Contig': 'ContigWithFilePositionOffset',
'reference_length': 8,
'best_snps': 0,
'all_passed_coverage': 8,
'reference_duplicated': 0,
'all_passed_consensus': 8,
'all_called': 8,
'any_snps': 0
})
observed_analysis_stats, observed_contig_stats = self.analysis.analyze_contig(
self.coroutine_fn, self.sample_groups, self.dups_contig,
self.reference_contig)
self.assertEqual(expected_analysis_stats, observed_analysis_stats)
self.assertEqual(expected_contig_stats, observed_contig_stats)
def setUp(self):
self.analysis = GenomeAnalysis(10, 0.9)
class AnalyzePositionTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
pass
def setUp(self):
self.analysis = GenomeAnalysis(10, 0.9)
def tearDown(self):
pass
@unittest.skip('Not Implemented')
def test_it_filters_position_by_coverage(self):
"""
Change the coverage to check for a hardcoded value.
"""
self.analysis.analyze_position((), (), ())
@unittest.skip('Not Implemented')
def test_it_filters_position_by_proportion(self):
# Change the proportion to check for a hardcoded value.
self.analysis.analyze_position((), (), ())
def test_fasta_position(self):
reference_position = Position(call='G', coverage='-', proportion='-')
dups_position = Position(call='0', coverage='-', proportion='-')
samples = ((Position(call='G', coverage='-', proportion='-'),
Position(call='G', coverage='-', proportion='-')), )
expected = PositionInfo(
is_all_called=True,
is_reference_clean=True,
is_reference_duplicated=False,
is_all_passed_coverage=True,
is_all_passed_proportion=True,
is_all_passed_consensus=True,
is_all_quality_breadth=True,
is_best_snp=False,
all_sample_stats=[[
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
})
],
[
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
}),
Counter({
'called_reference': 1,
'passed_coverage_filter': 1,
'quality_breadth': 1,
'was_called': 1,
'passed_proportion_filter': 1,
'called_snp': 0,
'called_degen': 0
})
]],
is_missing_matrix=False,
called_reference=2,
called_snp=0,
passed_coverage_filter=2,
passed_proportion_filter=2,
num_A=0,
num_C=0,
num_G=2,
num_T=0,
num_N=0,
call_str=['G', 'G', 'G'],
masked_call_str=['G', 'G', 'G'],
CallWasMade='YY',
PassedDepthFilter='--',
PassedProportionFilter='--',
Pattern=['1', '1', '1'])
self.assertEqual(
expected,
self.analysis.analyze_position(reference_position, dups_position,
samples))
def setUpClass(cls):
cls.analysis = GenomeAnalysis(10, 0.9)
def setUp(self):
vcf = StringIO(initial_value='')
fasta = StringIO(initial_value='')
self.analysis = GenomeAnalysis(10, 0.9)