def test_should_obtain_correct_vcf_header_on_reduce(self):
temp_vcf_filename_b = self.__run_wecall_variant_caller(
"2",
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT",
["............T........................C...."], vcf_stem="ab"
)
temp_vcf_filename_a = self.__run_wecall_variant_caller(
"1",
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT",
["...................T......................"], vcf_stem="aa"
)
with VCFReaderContextManager(temp_vcf_filename_a) as temp_vcf_a:
with VCFReaderContextManager(temp_vcf_filename_b) as temp_vcf_b:
temp_vcf_a.read_header()
header_a = temp_vcf_a.header
temp_vcf_b.read_header()
header_b = temp_vcf_b.header
self.__run_wecall_reduce()
with VCFReaderContextManager(self.final_vcf_location) as final_vcf:
final_vcf.read_header()
expected_header = header_a
expected_header.set_contig('2', header_b.get_contig('2').length)
self.assertEqual(final_vcf.header, expected_header)
def test_should_derive_use_lexigraphical_order_of_vcfs_for_reduce(self):
temp_vcf_filename_b = self.__run_wecall_variant_caller(
"2",
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT",
["............T........................C...."], vcf_stem="ab"
)
temp_vcf_filename_a = self.__run_wecall_variant_caller(
"1",
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT",
["...................T......................"], vcf_stem="aa"
)
with VCFReaderContextManager(temp_vcf_filename_a) as temp_vcf_a:
with VCFReaderContextManager(temp_vcf_filename_b) as temp_vcf_b:
# aa is lexicographical less than ab
reference_records = list(
temp_vcf_a.read_records()) + list(temp_vcf_b.read_records())
self.__run_wecall_reduce()
with VCFReaderContextManager(self.final_vcf_location) as final_vcf:
final_records = list(final_vcf.read_records())
self.assertEqual(len(final_records), 3)
self.assertEqual(final_records, reference_records)
def __run_small_variant_caller(self, refcalls, format):
sample_bank = SampleBank("T")
sample_bank.add_sample_name("TEST").add_sequence(".")
variant_caller_builder = VariantCallerBuilderFromSampleBank(
sample_bank, self.work_dir)
variant_caller_builder.configuration = {} # clear config.
variant_caller = variant_caller_builder.build()
variant_caller.add_additional_command('outputRefCalls', refcalls)
variant_caller.add_additional_command('outputFormat',
"VCF{}".format(format))
variant_caller.run()
with VCFReaderContextManager(variant_caller.output_vcf) as vcf_file:
actual_schema = vcf_file.read_header()
reference = os.path.splitext(
os.path.basename(variant_caller_builder.wecall_input_data.
reference_filename))[0]
expected_schema = wecall_schema(
file_date=datetime.datetime.today().strftime('%F'),
reference=reference,
contigs={
sample_bank.reference.chrom: {
"length": sample_bank.reference.length_minus_deletions()
}
},
add_ref_calls=refcalls,
format=format)
return expected_schema, actual_schema
def test_read_variant_from_vcf(self):
with VCFReaderContextManager(
os.path.join(self.data_dir, "vcf_example.vcf")) as vcf_handler:
variant_gen = (record.variant
for record in vcf_handler.read_records())
next_variant = next(variant_gen)
self.assertEqual(next_variant.chrom, "20")
self.assertEqual(next_variant.pos_from, 9)
self.assertEqual(next_variant.ref, "CT")
self.assertEqual(next_variant.alt, "C")
def test_should_reduce_a_wecall_produced_vcf_to_a_valid_vcf(self):
temp_vcf_filename = self.__run_wecall_variant_caller(
"1",
"AAAAAAAAAAACGCACCCCCCATAAAAAAAATTTTTTTTTTT",
["...................T......................"],
)
with VCFReaderContextManager(temp_vcf_filename) as temp_vcf:
reference_header = temp_vcf.header
reference_records = list(temp_vcf.read_records())
self.__run_wecall_reduce()
with VCFReaderContextManager(self.final_vcf_location) as final_vcf:
self.assertEqual(final_vcf.header, reference_header)
final_records = list(final_vcf.read_records())
self.assertEqual(len(final_records), 1)
self.assertEqual(final_records, reference_records)
def __init__(self, test_case, path):
self.__test_case = test_case
self.__path = path
self.__test_case.assertTrue(os.path.exists(self.__path))
with VCFReaderContextManager(self.__path) as vcf_reader:
self.__schema = vcf_reader.read_header()
self.__records = list(vcf_reader.read_records())
# ensure genotype likelihoods are within range throughout
for record in self.__records:
for sample_name in record.sample_info.get_sample_names():
try:
for GL_value in record.sample_info.get_field(
sample_name, 'GL'):
self.__test_case.assertTrue(GL_value <= 0.0)
except KeyError:
pass
def test_reads_simple_file(self):
filename = os.path.join(self.work_dir, "test.vcf")
with VCFWriterContextManager(filename) as left_vcf:
left_vcf.write_variant(Variant("1", 1, "A", "T"))
left_vcf.write_variant(Variant("2", 1, "A", "T"))
left_vcf.write_variant(Variant("10", 1, "A", "T"))
expected_variants = [
Variant("1", 1, "A", "T"),
Variant("2", 1, "A", "T"),
Variant("10", 1, "A", "T"),
]
with VCFReaderContextManager(filename) as vcf_reader:
actual_variants = [record.variant for record in vcf_reader.read_records()]
self.assertEqual(expected_variants, actual_variants)
def test_should_write_missing_values_in_sample_data(self):
with VCFReaderContextManager(
os.path.join(self.data_dir, "vcf_example.vcf")) as vcf_handler:
first_record = next(vcf_handler.read_records())
sample_data = SampleData(['GT', 'PL', 'GQ'],
['sample1', 'sample2', 'sample3'])
sample_data.add_sample_data("sample1", "GT", GenotypeCall("1|0"))
sample_data.add_sample_data("sample1", "PL", [3000, 0, 3000])
sample_data.add_sample_data("sample1", "GQ", [1000])
sample_data.add_sample_data("sample2", "GT", GenotypeCall("1|1"))
sample_data.add_sample_data("sample2", "PL", [2000, 0, 1000])
sample_data.add_sample_data("sample2", "GQ", [3])
first_record.sample_info = sample_data
print((sample_data.to_vcf_columns()))
vcf_string = vcf_row_from_record(first_record)
expected_vcf_string = "20 10 . CT C 3000 PASS PP=3000;DP=250;DPR=140;DPF=110;VC=100;VCR=49;VCF=51;ABPV=0.2;SBPV=0.3;MQ=70.0;BR=31.0;QD=None GT:PL:GQ 1|0:3000,0,3000:1000 1|1:2000,0,1000:3 ./.:.:." # noqa
self.assertEqual(expected_vcf_string, vcf_string)
def test_read_record_line(self):
with VCFReaderContextManager(
os.path.join(self.data_dir, "vcf_example.vcf")) as vcf_handler:
record_gen = vcf_handler.read_records()
next_record = next(record_gen)
self.assertEqual(next_record.chrom, "20")
self.assertEqual(next_record.pos_from, 9)
self.assertEqual(next_record.ids, set())
self.assertEqual(next_record.ref, "CT")
self.assertEqual(next_record.alt, "C")
self.assertEqual(next_record.quality, 3000)
self.assertEqual(next_record.filters, set())
self.assertEqual(next_record.passes_filter, True)
self.assertEqual(next_record.from_multi_alt, False)
self.assertEqual(next_record.type, variant.TYPE_DEL)
self.assertEqual(next_record.info['PP'], [3000])
self.assertEqual(next_record.info['DP'], [250])
self.assertEqual(next_record.info['VC'], [100])
self.assertEqual(next_record.info['ABPV'], [0.2])
self.assertEqual(next_record.info['SBPV'], [0.3])
self.assertEqual(next_record.info['MQ'], [70])
self.assertEqual(next_record.info['QD'], [None])
self.assertTrue(next_record.sample_info.has_sample("sample1"))
self.assertEqual(next_record.genotypes, {
"sample1": GenotypeCall("1|0"),
"sample2": GenotypeCall("1|1")
})
self.assertEqual(
next_record.sample_info.get_field("sample1", 'GT'),
GenotypeCall("1|0"))
self.assertEqual(
next_record.sample_info.get_field("sample1", 'PL'),
[3000, 0, 3000])
self.assertEqual(
next_record.sample_info.get_field("sample1", "GQ"), [1000])
def __get_example_schema(self, filename):
with VCFReaderContextManager(os.path.join(self.data_dir,
filename)) as vcf_handler:
vcf_handler.read_header()
return vcf_handler.header