def test_should_fail_if_invalid_output_file_format_provided(self):
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_output_format('bah4.1')
svc_driver.call(False).with_incorrect_output_format_error()
def test_should_fail_if_mem_limit_is_negative(self):
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_mem_limit(-100) \
.with_output_vcf_filename(self.output_filename)
svc_driver.call(False).with_mem_limit_range_error()
def test_should_fail_if_mem_limit_is_just_above_acceptable_range(self):
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_mem_limit(1024 * 1024 + 1) \
.with_output_vcf_filename(self.output_filename)
svc_driver.call(False).with_mem_limit_range_error()
def test_should_not_fail_due_to_existing_output_if_overwrite_specified(
self):
open(self.output_filename, "w").close()
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_overwrite(True) \
.with_output_vcf_filename(self.output_filename)
svc_driver.call(expected_success=True)
def test_get_unknown_quality_if_no_reads_span_region(self):
chrom = "1"
driver = SVCDriver(self)
driver.with_ref_sequence(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", chrom=chrom
).with_read(
" ",
).with_output_ref_calls(True)
driver.call().with_output_vcf().has_record(chrom, 0, "A", ref_alt).with_quality(None)
def test_should_run_if_interval_not_contained_in_reference(self):
svc = SVCDriver(self)
svc.with_ref_sequence(
"ACGTACGTACGTACGTACGTACGT", chrom="1"
).with_read(
"....G...................", chrom="1"
).with_bed_file(
['1\t24\t28']
).with_region_padding(0)
svc.call(True).with_output_vcf().record_count(0)
def test_should_have_standard_set_of_info_keys_for_variant(self):
svc_driver = SVCDriver(self)\
.with_ref_sequence(
"TAGAATTGTTTGAGCTCTTTGTATTTCCTGTTATTAATCCCTTGTCAGAAGGGTCGTTTG", )\
.with_read(
"....................A.......................................", n_fwd=3, n_rev=0)
svc_driver.call()\
.with_output_vcf()\
.record_count(1)\
.has_record_for_variant(Variant("1", 20, "G", "A"))\
.with_info()\
.has_keys("PP", "DP", "DPR", "DPF", "VC", "VCR", "VCF", "ABPV", "SBPV", "MQ", "QD", "BR")
def test_should_fail_if_output_already_exists_serial(self):
open(self.output_filename, "w").close()
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_overwrite(False) \
.with_output_vcf_filename(self.output_filename)
assert (os.path.exists(self.output_filename))
svc_driver.call(expected_success=False).output_exists_error(
self.output_filename)
def test_should_cope_with_region_padding_which_pads_to_negative_index_into_reference(self):
svc = SVCDriver(self)
svc.with_ref_sequence(
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCCCCCCCCCCCATG", chrom='1'
).with_read(
"......................................................", chrom='1', n_fwd=10, n_rev=10
).with_read(
" ...............................G.......... ", chrom='1', n_fwd=10, n_rev=10
).with_read(
" ..............................T........... ", chrom='1', n_fwd=6, n_rev=6)
svc.with_region_string('1:20-41')
svc.with_region_padding(20)
svc.call(expected_success=True)
def test_raises_if_genotyping_file_doesnt_exist(self):
missing_file = join(
self.work_dir,
"I_DONT_EXIST_NOT_JUST_IN_THE_PHILOSOPHICAL_SENSE.vcf.gz")
driver = SVCDriver(self)
driver.with_ref_sequence("ACGCCCCCTGCAAAAAAAAAA", ).with_read(
"....G................",
n_fwd=5,
n_rev=5,
).with_genotype_alleles(missing_file).with_verbosity(0)
driver.call(expected_success=False)\
.missing_genotype_file(missing_file)
def test_should_not_fail_due_to_existing_output_if_no_option_specified_in_parallel(
self):
open(self.output_filename, "w").close()
svc_driver = SVCDriver(self)
svc_driver \
.with_ref_sequence("A") \
.with_read(".") \
.with_number_of_jobs(2) \
.with_work_dir(self.we_call_work_dir) \
.with_output_vcf_filename(self.output_filename)
assert (os.path.exists(self.output_filename))
svc_driver.call(expected_success=True)
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_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_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_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_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_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_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_bad_reads_filter_not_applied_if_one_sample_is_not_naughty(self):
svc = SVCDriver(self)
svc.with_var_filters("BR")
svc.with_bad_reads_window_size(7)
svc.with_min_bad_reads_score(13)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
" 3333333 3333333 ",
sample_name="GOOD",
n_rev=2,
n_fwd=2).with_read(
"................G...........................",
" 0000000 0000000 ",
sample_name="BAD",
n_rev=10,
n_fwd=10).with_read(
"................G...........................",
" 00000 0000 ",
sample_name="UGLY",
n_rev=10,
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_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_not_apply_bad_reads_to_insertion_if_all_supporting_reads_have_high_base_qualities(
self):
svc = SVCDriver(self) \
.with_var_filters("BR") \
.with_bad_reads_window_size(3) \
.with_min_bad_reads_score(15)
svc.with_ref_sequence(
# 1234567890123 456789
"AAAGCGTACAACCG*GGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"..............*..G...........................",
" 1 ",
n_rev=11,
n_fwd=10)
svc.with_read("..............T..............................",
n_rev=10,
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, 13, "G", "GT")) \
.with_no_filters()
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_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_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_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_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_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_use_read_evidence_outside_region_to_not_call_snp(self):
svc = SVCDriver(self)
# If no region was specified then only the SNP with stronger evidence
# would be outputted.
svc.with_ref_sequence(
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCCCCCCCCCCCATG",
chrom='1').with_read(
"......................................................",
chrom='1',
n_fwd=10,
n_rev=10).with_read(
" ...............................G.......... ",
chrom='1',
n_fwd=10,
n_rev=10
).with_read(
" ..............................T........... ",
chrom='1',
n_fwd=6,
n_rev=6)
svc.with_region_string('1:0-41')
expect = svc.call()
expect.with_output_vcf().record_count(0)
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)