def test_phasing_for_two_heterozygous_variants_ocrn_same_strand(self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self) \
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom) \
.with_read(
"........T...T........", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_output_phased_genotypes(True) \
.with_allow_MNP_calls(False)
vcf_expect = svc_driver.call()\
.with_output_vcf()\
.record_count(2)
records_expect = vcf_expect.has_record_for_variants(
Variant(chrom, 8, "G", "T"),
Variant(chrom, 12, "A", "T")
)
records_expect\
.with_sample(sample_name)\
.has_phased_genotypes("0|1", "0|1")\
.has_phase_set_id("8")
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_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_should_not_apply_filter_to_snp_if_all_supporting_reads_are_good(
self):
svc = SVCDriver(self) \
.with_var_filters("BR") \
.with_bad_reads_window_size(7) \
.with_min_bad_reads_score(15)
svc.with_ref_sequence(
# 1234567 890123456789
"AAAGCGTAA**CCGGGTTAGT**CAAACCCGTTACGTATGCATG").with_read(
".........**.....G....**.....................",
n_rev=10,
n_fwd=10).with_read(
".........GT..........TA.....................",
" 00 00 ",
n_rev=11,
n_fwd=10)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(3)
vcf_expectation \
.has_record_for_variant(Variant(DEFAULT_CHROM, 14, "T", "G")) \
.with_no_filters()
def test_calls_deletion_and_snp_at_same_location_in_repeat_region_with_few_reads_as_anchors(
self):
chrom = "1"
sample = "sample"
svc_driver = SVCDriver(self)
svc_driver.with_ref_sequence(
'CGAGAGAGAGAGAGAGAGAGATAGAGAGAGAGAGAGAGAGTC',
chrom=chrom).with_read(
'....................**....................',
n_rev=5,
n_fwd=0,
chrom=chrom,
sample_name=sample).with_read(
'.....................G....................',
n_rev=5,
n_fwd=0,
chrom=chrom,
sample_name=sample)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect \
.has_record_for_variants(
Variant(chrom, 21, "T", "G"),
Variant(chrom, 19, "GAT", "G")
).with_sample(sample).has_phased_genotypes(".|1", "1|.")
def test_phase_alignment_for_het_variants_for_three_clusters_when_first_cluster_is_homozygous(
self):
sample_name = "sample1"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCCTGGGGGGGGGTGGGGGGGGGGGCAAAAAAAAAA", chrom=chrom) \
.with_read(
"....A....................................", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
"....A.............C...............T......", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_output_phased_genotypes(True) \
.with_allow_MNP_calls(False) \
.with_max_cluster_distance(5) \
.with_min_cluster_distance(5)
vcf_expect = svc_driver.call()\
.with_output_vcf()\
.record_count(3)
vcf_expect.has_record_for_variants(Variant(chrom, 4, "C", "A"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|1")\
.has_phase_set_id("4")
vcf_expect.has_record_for_variants(Variant(chrom, 18, "T", "C"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|0")\
.has_phase_set_id("13")
vcf_expect.has_record_for_variants(Variant(chrom, 34, "A", "T"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|0")\
.has_phase_set_id("13")
def test_phase_not_aligns_for_hom_snp_in_first_cluster(self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCCTGGGGGGGGGTGGGGGGGGGGGCAAAAAAAAAA", chrom=chrom) \
.with_read(
".......A.....................A...........", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
".......A.................................", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_output_phased_genotypes(True) \
.with_allow_MNP_calls(False) \
.with_max_cluster_distance(10)
vcf_expect = svc_driver.call()\
.with_output_vcf()\
.record_count(2)
vcf_expect.has_record_for_variants(Variant(chrom, 7, "C", "A"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|1")\
.has_phase_set_id("7")
vcf_expect.has_record_for_variants(Variant(chrom, 29, "G", "A"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|0")\
.has_phase_set_id("28")
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 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_calls_correct_reference_between_clusters_with_uncalled_indel_between(
self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAATAACGCACGCCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..*....................... ",
n_fwd=10,
n_rev=10).with_read(
".......................*............ ",
n_fwd=1,
n_rev=1).with_read(
".......................T.. ",
n_fwd=10,
n_rev=10).with_output_ref_calls(
True).with_max_cluster_distance(5)
expect = driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.has_reference_calls(ChromInterval(chrom, 0, 8))
vcf_expect.has_record_for_variant(Variant(chrom, 8, "TA", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 10, 23))
vcf_expect.has_record_for_variant(Variant(chrom, 23, "A", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 24, 41))
def test_dont_call_reference_between_variant_and_insertion_due_to_vcf_rep_issues(
self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAACGCACG*CCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..........T................ ",
chrom=chrom).with_read(
" ...............T........... ",
chrom=chrom).with_read(
" ...........T.*................ ",
chrom=chrom).with_read(
" ...........T.*..................... ",
chrom=chrom).with_read(
"...............T.*......... ",
chrom=chrom).with_output_ref_calls(True)
vcf_expect = driver.call().with_output_vcf()
# Has only 4 records which are:-
vcf_expect.has_reference_calls_for_region(chrom, 0, 15)
vcf_expect.has_record(chrom, 15, "C", "T")
vcf_expect.has_record(chrom, 16, "G", "GT")
vcf_expect.has_reference_calls_for_region(chrom, 17, 41)
def test_calls_reference_on_location_with_low_quality_variant_support(
self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAATAACGCACGCCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..*....................... ", n_fwd=2,
n_rev=1).with_read(
".................T.....T......... ",
" 1 ",
n_fwd=1,
n_rev=1).with_read(
".......................T.. ",
n_fwd=1,
n_rev=0).with_output_ref_calls(True)
expect = driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.has_reference_calls(ChromInterval(chrom, 0, 8))
vcf_expect.has_record_for_variant(Variant(chrom, 8, "TA", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 10, 23))
vcf_expect.has_record_for_variant(Variant(chrom, 23, "A", "T"))
vcf_expect.has_reference_calls(ChromInterval(chrom, 24, 41))
def test_calls_correct_ref_calls_with_cluster_of_variants(self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAATAACGCACG*CCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..*.......*................ ",
chrom=chrom).with_read(
" .......*.......*........... ",
chrom=chrom).with_read(
" .............T......T.......... ",
chrom=chrom).with_read(
" .............T......T.............. ",
chrom=chrom).with_read(
".................T......T.. ",
chrom=chrom).with_output_ref_calls(True)
vcf_expect = driver.call().with_output_vcf()
vcf_expect.has_reference_calls_for_region(chrom, 0, 8)
vcf_expect.has_record(chrom, 8, "TA", "T")
vcf_expect.has_reference_calls_for_region(chrom, 10, 16)
vcf_expect.has_record(chrom, 16, "G", "GT")
vcf_expect.has_reference_calls_for_region(chrom, 17, 23)
vcf_expect.has_record(chrom, 23, "A", "T")
vcf_expect.has_reference_calls_for_region(chrom, 24, 41)
def test_calls_ref_calls_correctly_with_mnp_that_contains_snp(self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAACGCACCCCCCATAAAAAAATTTTTTTTTTT",
chrom=chrom).with_read(
" ..........TTTT............. ",
chrom=chrom).with_read(
" ...............TTTT........ ",
chrom=chrom).with_read(
" ..............T................ ",
chrom=chrom).with_read(
" ..............T.................... ",
chrom=chrom).with_read(
"..................T........ ",
chrom=chrom).with_output_ref_calls(
True).with_allow_MNP_calls(True)
vcf_expect = driver.call().with_output_vcf()
vcf_expect.has_reference_calls_for_region(chrom, 0, 17)
vcf_expect.has_record(chrom, 17, "CCCC", "TTTT")
vcf_expect.has_record(chrom, 18, "C", "T")
vcf_expect.has_reference_calls_for_region(chrom, 21, 41)
def test_depth_computation_all_reads_spanning_reference_with_insertion(
self):
sample_name = "bah"
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAAAAAAC*AAAAAAAAAAAAAAAAAAAAAAA", chrom=chrom).with_read(
"................T.......................",
n_rev=5,
n_fwd=5,
sample_name=sample_name).with_output_ref_calls(
True).with_allow_MNP_calls(False)
expect = driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect \
.has_record_for_variant(Variant(chrom, 0, "A", ref_alt))\
.with_sample(sample_name).has_read_depth(10).has_min_read_depth(10)
vcf_expect \
.has_record_for_variant(Variant(chrom, 15, "C", "CT"))\
.with_sample(sample_name).has_read_depth(10)
vcf_expect \
.has_record_for_variant(Variant(chrom, 16, "A", ref_alt))\
.with_sample(sample_name).has_read_depth(10).has_min_read_depth(10)
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_phasing_for_isolated_snp_on_one_sample_only(self):
sample_1 = "sample_1"
sample_2 = "sample_2"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom
).with_read(
"........T............", n_fwd=10, n_rev=10, sample_name=sample_1
).with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_2
)
svc_driver.with_output_phased_genotypes(True)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.record_count(1)
record_expect = vcf_expect.has_record_for_variant(
Variant(chrom, 8, "G", "T"))
sample_1_expect = record_expect.with_sample(sample_1)
sample_1_expect.has_phased_genotype("1|1")
sample_1_expect.has_phase_set_id(str(8))
sample_1_expect.has_phase_set_quality(MAX_PHRED)
sample_2_expect = record_expect.with_sample(sample_2)
sample_2_expect.has_phased_genotype("0|0")
sample_2_expect.has_phase_set_id(str(8))
sample_2_expect.has_phase_set_quality(MAX_PHRED)
def test_should_report_unkown_value_for_allele_frequence_when_depth_is_zero(
self):
# Only way to output depth zero for sample and variant is to have
# another good sample
good_sample = "good_sample"
empty_sample = "empty_sample"
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence("AAACGTAGCTGTGCACCCCCAAA",
chrom=chrom).with_read(
"..........T............",
n_fwd=10,
n_rev=10,
sample_name=good_sample,
).with_read(
".......................",
n_fwd=0,
n_rev=0,
sample_name=empty_sample,
)
vcf = driver.call().with_output_vcf()
vcf \
.with_samples([good_sample, empty_sample]) \
.record_count(1)
vcf \
.has_record_for_variant(Variant(chrom, 10, "G", "T")) \
.with_sample(empty_sample) \
.has_read_depth(0) \
.has_variant_allelic_frequency(None)
def test_phase_alignment_for_two_snps_in_different_clusters_on_different_strands(
self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCCTGGGGGGGGGTGGGGGGGGGGGCAAAAAAAAAA", chrom=chrom) \
.with_read(
".......A.................................", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
".............................A...........", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_output_phased_genotypes(True) \
.with_max_cluster_distance(10) \
vcf_expect = svc_driver.call()\
.with_output_vcf()\
.record_count(2)
vcf_expect.has_record_for_variants(Variant(chrom, 7, "C", "A"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("1|0")\
.has_phase_set_id("7")
vcf_expect.has_record_for_variants(Variant(chrom, 29, "G", "A"))\
.with_sample(sample_name)\
.has_exact_phased_genotypes("0|1")\
.has_phase_set_id("7")
def test_should_record_the_read_support_insertion_and_snp_on_same_strand(
self):
sample = "sample"
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence("AAACGTAGCTG*GCACCCCCAAA",
chrom=chrom).with_read(
"...........*...........",
n_fwd=10,
n_rev=10,
sample_name=sample,
).with_read(
"..........CT...........",
n_fwd=10,
n_rev=10,
sample_name=sample,
)
vcf = driver.call().with_output_vcf()
vcf \
.with_samples([sample]) \
.record_count(2)
vcf \
.has_record_for_variant(Variant(chrom, 9, 'T', 'TC')) \
.with_sample(sample) \
.has_read_depth(40) \
.has_allelic_read_support(20, 20) \
.has_genotype("0/1")
def test_calls_correct_reference_when_one_sample_has_snp_and_tother_has_indel(self):
chrom = "1"
sample_1 = "sample_1"
sample_2 = "sample_2"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAACGCACG*CCCCATAAAAAAATTTTTTTTTTT", chrom=chrom
).with_read(
" ..........T................ ", chrom=chrom, sample_name=sample_1
).with_read(
" ...............T........... ", chrom=chrom, sample_name=sample_1
).with_read(
" ...........T.*................ ", chrom=chrom, sample_name=sample_2
).with_read(
" ...........T.*..................... ", chrom=chrom, sample_name=sample_2
).with_read(
"...............T.*......... ", chrom=chrom, sample_name=sample_2
).with_output_ref_calls(True)
vcf_expect = driver.call().with_output_vcf()
# Has only 4 records which are:-
vcf_expect.has_reference_calls_for_region(chrom, 0, 15)
vcf_expect.has_record(chrom, 15, "C", "T")
vcf_expect.has_record(chrom, 16, "G", "GT")
vcf_expect.has_reference_calls_for_region(chrom, 17, 41)
def test_should_count_reads_that_do_not_overlap_the_calling_region(self):
sample = "seed"
chrom = "1"
driver = SVCDriver(self).with_allow_MNP_calls(True)
driver.with_ref_sequence(
"GAAAAAAAAAAACGCACCCCCAAATTTTTTTTAA***********AAAATAAAAAACGCACCCCCAAATTTTTTTTAA",
chrom=chrom
).with_read(
" ..........G......................",
n_fwd=10,
n_rev=10,
sample_name=sample,
).with_read(
"..................................AAAATAAAAAG ",
n_fwd=10,
n_rev=10,
sample_name=sample,
).with_region_string("{}:{}-{}".format(chrom, 34, 55))
vcf = driver.call().with_output_vcf()
vcf \
.has_record_for_variant(Variant(chrom, 44, 'A', 'G')) \
.with_info() \
.with_field("DP", [40]) \
.with_field("VC", [40])
def test_bad_reads_filter_not_applied_when_median_read_is_good(self):
svc = SVCDriver(self) \
.with_var_filters("BR") \
.with_bad_reads_window_size(7) \
.with_min_bad_reads_score(20)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
" 1 1 ",
n_rev=10,
n_fwd=10).with_read(
"................G...........................",
" 4444444 4444444 ",
n_rev=11,
n_fwd=10)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
vcf_expectation \
.has_record_for_variant(Variant(DEFAULT_CHROM, 16, "T", "G")) \
.with_no_filters()
def test_should_stop_mildly_allele_and_strand_biased_calls(self):
chrom = 'chr1'
svc = SVCDriver(self)
reads = 10
allele_bias = 5
strand_bias = 4
svc.with_ref_sequence(
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG",
chrom=chrom).with_read(
"............................................",
n_rev=reads + allele_bias + strand_bias,
n_fwd=reads + allele_bias - strand_bias,
chrom=chrom).with_read(
"................G...........................",
n_rev=reads - allele_bias - strand_bias,
n_fwd=reads - allele_bias + strand_bias,
chrom=chrom)
expect = svc.call()
expect.with_output_vcf() \
.record_count(1) \
.has_record_for_variant(Variant(chrom, 16, 'T', 'G')) \
.with_filters({'AB+SB'})
def test_should_call_basic_snps(self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self).with_ref_sequence(
"GCCCCAGCCTCCCAAAGTGCATTGATTTTGTTGTTGTTGTGCTTATTTGCACTCCAGCCTGGCCTCTCCTTTCTTG",
chrom=chrom
).with_read(
"...............T.........A...............G..................................",
n_fwd=10,
n_rev=10,
sample_name=sample_name
).with_read(
".........................A..........................A.......................",
n_fwd=10,
n_rev=10,
sample_name=sample_name).with_normalize_variant_calls(True)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.record_count(4)
vcf_expect.has_record(chrom, 15, "A",
"T").with_sample(sample_name).has_genotype("1|0")
vcf_expect.has_record(chrom, 25, "T",
"A").with_sample(sample_name).has_genotype("1|1")
vcf_expect.has_record(chrom, 41, "C",
"G").with_sample(sample_name).has_genotype("1|0")
vcf_expect.has_record(chrom, 52, "T",
"A").with_sample(sample_name).has_genotype("0|1")
def test_min_depth_computation_with_mixed_depth_of_reads(self):
sample_name = "bah"
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", chrom=chrom).with_read(
".............................. ",
n_rev=5,
n_fwd=5,
sample_name=sample_name).with_read(
" ..............................",
n_rev=3,
n_fwd=3,
sample_name=sample_name).with_output_ref_calls(True)
expect = driver.call()
expect\
.with_output_vcf()\
.has_record_for_variant(Variant(chrom, 0, "A", ref_alt))\
.with_sample(sample_name).has_read_depth(10).has_min_read_depth(10)
expect\
.with_output_vcf()\
.has_record_for_variant(Variant(chrom, 10, "A", ref_alt))\
.with_sample(sample_name).has_read_depth(16).has_min_read_depth(16)
expect\
.with_output_vcf()\
.has_record_for_variant(Variant(chrom, 30, "A", ref_alt))\
.with_sample(sample_name).has_read_depth(6).has_min_read_depth(6)
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_min_depth_computation_with_mixed_depth_of_reads_when_no_chunking_occurs(
self):
sample_name = "bah"
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", chrom=chrom).with_read(
"........................................",
n_rev=10,
n_fwd=10,
sample_name=sample_name).with_read(
"................................... ",
n_rev=2,
n_fwd=2,
sample_name=sample_name).with_read(
" ................................... ",
n_rev=1,
n_fwd=1,
sample_name=sample_name).with_output_ref_calls(True)
expect = driver.call()
expect\
.with_output_vcf()\
.has_record_for_variant(Variant(chrom, 0, "A", ref_alt))\
.with_sample(sample_name)\
.has_read_depth(round(20 + 4 * 35 / 40 + 2 * 35 / 40))\
.has_min_read_depth(20)
def test_should_call_variants(self):
chrom = 'chr1'
sample_name = 'sample'
svc = SVCDriver(self) \
.with_ploidy(3)
svc.with_ref_sequence(
"AAAGCGTACAACCGGGTTAGTC***AACCCGTTACGTATGCATG", chrom=chrom
).with_read(
"......C.........G.....ATG.......***.........", n_rev=10, n_fwd=10, chrom=chrom, sample_name=sample_name
).with_read(
"......C...............ATG.......***.........", n_rev=10, n_fwd=10, chrom=chrom, sample_name=sample_name
).with_read(
"......................ATG.......***.........", n_rev=10, n_fwd=10, chrom=chrom, sample_name=sample_name)
expect = svc.call()
vcf = expect \
.with_output_vcf() \
.record_count(4)
vcf.has_record_for_variant(Variant(chrom, 6, 'T', 'C')).with_sample(sample_name).has_genotype('0/1/1')
vcf.has_record_for_variant(Variant(chrom, 16, 'T', 'G')).with_sample(sample_name).has_genotype('0/0/1')
vcf.has_record_for_variant(Variant(chrom, 21, 'C', 'CATG')).with_sample(sample_name).has_genotype('1/1/1')
vcf.has_record_for_variant(Variant(chrom, 28, 'TTAC', 'T')).with_sample(sample_name).has_genotype('1/1/1')
def test_phasing_for_isolated_heterozygous_variant(self):
sample_name = "a_sample"
chrom = "1"
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"ACGCCCCTGCAAAAAAAAAAT", chrom=chrom) \
.with_read(
"........T............", n_fwd=10, n_rev=10, sample_name=sample_name) \
.with_read(
".....................", n_fwd=10, n_rev=10, sample_name=sample_name)
svc_driver.with_output_phased_genotypes(True)
expect = svc_driver.call()
vcf_expect = expect.with_output_vcf()
vcf_expect.record_count(1)
record_expect = vcf_expect.has_record_for_variants(
Variant(chrom, 8, "G", "T"))
sample_expect = record_expect.with_sample(sample_name)
sample_expect.has_phased_genotypes("0|1")
sample_expect.has_phase_set_id(str(8))
sample_expect.has_phase_set_quality(MAX_PHRED)