def test_raises_if_genotyping_file_is_not_expected_format(self):
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.build() # note: not compressed or indexed
driver = SVCDriver(self)
driver.with_ref_sequence("ACGCCCCCTGCAAAAAAAAAA", ).with_read(
"....G................",
n_fwd=5,
n_rev=5,
).with_genotype_alleles(gv_builder.filename).with_verbosity(0)
driver.call(expected_success=False)\
.unexpected_genotype_file_format(gv_builder.filename)
def test_should_handle_complex_variant_input(self):
chrom = "22"
variant = Variant(chrom, 10, "CAA", "CA")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call()
expect.with_log()\
.input_variant_trimmed_warning(variant, Variant(chrom, 11, "A", ""))
expect.with_output_vcf()\
.record_count(1)
def test_doesnt_give_a_flying_damn_about_spurious_filters(self):
chrom = "22"
variant = Variant(chrom, 11, "A", "C")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant,
filters={"#$.:@$%$%^&**()7!"})
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call(expected_success=True)
expect.with_output_vcf()\
.has_record_for_variant(variant)\
.with_sample(dodgy_sample)\
.has_genotype("1/1")
def test_doesnt_give_a_flying_damn_about_spurious_filter_header(self):
chrom = "22"
variant = Variant(chrom, 11, "A", "C")
schema = Schema()
complex_filter_name = '.+-*\\/~@?!%^&><=\"\'(){}[]_|'
schema.set_filter(complex_filter_name, 'unusual characters')
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"),
schema=schema)
gv_builder.with_record_from_variant(variant,
filters={complex_filter_name})
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call(expected_success=True)
expect .with_output_vcf()\
.has_record_for_variant(variant)\
.with_sample(dodgy_sample)\
.has_genotype("1/1")
def test_genotypes_mnp_correctly_with_supporting_reads(self):
chrom = "22"
variant = Variant(chrom, 11, "AAA", "CAC")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.C.......",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call()
expect.with_output_vcf()\
.has_record_for_variant(variant)\
.with_sample(dodgy_sample)\
.has_genotype("./1")
def test_genotypes_variant_correctly_complex_indel_which_is_snp_and_deletion(
self):
chrom = "22"
variant = Variant(chrom, 10, "CA", "T")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
sample = "bobs_your_uncle"
driver.with_ref_sequence("ACGCCCCCTGCAAAAAAAAAAA",
chrom=chrom,
pos_from=0).with_read(
"..........T*..........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call()
expect.with_output_vcf()\
.has_record_for_variant(variant)\
.with_sample(sample)\
.has_genotype("1/1")
def test_gets_correct_genotype_if_not_fully_left_aligned(self):
chrom = "22"
variant = Variant(chrom, 12, "AA", "A")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAATACGCCCCCTACGCCCCCT", chrom=chrom,
pos_from=0).with_read(
"...................*...................",
n_fwd=10,
n_rev=10,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call()
expect.with_output_vcf()\
.record_count(1)\
.has_record_for_variant(variant)\
.with_sample(dodgy_sample).has_genotype("1/1")
def calls_variants(self, ref, sequence_list, candidate_ascii_haplotypes, prior, expected_ascii_haplotypes):
sample_bank = SampleBank(ref)
sample_bank.add_sample_with_seqs_and_quals("TEST", sequence_list, 1, 0)
variant_generator = AsciiVariantGenerator(sample_bank.reference)
candidate_variants = variant_generator.get_variants(candidate_ascii_haplotypes)
expected_variants = variant_generator.get_variants(expected_ascii_haplotypes)
candidate_variant_list = VCFBuilder(path.join(self.work_dir, "candiate_variants.vcf"))
candidate_variant_list.schema.set_info_data('AF', 'A', 'Float', 'Allele Frequency')
for var in candidate_variants:
candidate_variant_list.with_record_from_variant(
var, info=InfoData(candidate_variant_list.schema, {"AF": prior})
)
candidate_variant_list.build().index()
vc_wrapper_builder = VariantCallerBuilderFromSampleBank(sample_bank, self.work_dir)
vc_wrapper_builder.configuration[CANDIDATE_VARIANTS_FILE_KEY] = candidate_variant_list.compressed_filename
callset = vc_wrapper_builder.build().run().get_variant_callset(self)
self.assertEqual(callset.get_variants(), set(expected_variants))
def test_raises_if_genotyping_file_not_indexed(self):
chrom = "22"
variant = Variant(chrom, 11, "A", "C")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().bgzip() # note: no index
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename).with_verbosity(0)
driver.call(expected_success=False)\
.missing_genotype_index_file(gv_builder.compressed_filename_index)
def test_should_have_zero_bad_reads_for_candidate_variant_with_no_reads_covering_variant(self):
chrom = "1"
candidate_variant_list = VCFBuilder(path.join(self.work_dir, "candiate_variants.vcf"))
candidate_variant_list.schema.set_info_data('AF', 'A', 'Float', 'Allele Frequency')
variant_1 = Variant(chrom, 30, 'T', 'C')
candidate_variant_list.with_record_from_variant(
variant_1, info=InfoData(candidate_variant_list.schema, {"AF": [0.72]}))
candidate_variant_list.build().index()
svc_driver = SVCDriver(self)\
.with_allow_MNP_calls(True)\
.with_ref_sequence(
"TGTTATTAATCCCTTGTCAGATGTTATTAATCCCTTGTCAGTCCCTTGTCAGT", chrom=chrom)\
.with_read(
"...........................C.. ......................", n_fwd=10, n_rev=10, sample_name='sample_1')\
.with_read(
" ", n_fwd=10, n_rev=10, sample_name='sample_2')\
.with_candidate_variants_file(candidate_variant_list.compressed_filename)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.missing_record_for_variant(variant_1)
def test_should_raise_if_output_ref_calls_is_switched_on(self):
chrom = "22"
variant = Variant(chrom, 10, "CAA", "CA")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename).with_output_ref_calls(True)
driver.call(
False
).genotyping_is_incompatible_with_outputting_reference_calls_error()
def test_doesnt_call_extra_variants(self):
chrom = "22"
variant = Variant("1", 11, "A", "C")
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"))
gv_builder.with_record_from_variant(variant)
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"....G................",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call()
expect \
.with_output_vcf() \
.record_count(0)