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_should_add_sequences_with_same_reference(self):
sample_bank = SampleBank("AAATTTTGGGGG")
sample_bank.add_sample_name("SAMPLE1")
sample_bank.add_sample_name("SAMPLE2")
self.assertEqual(sample_bank["SAMPLE1"].reference.ref_seq,
sample_bank["SAMPLE2"].reference.ref_seq)
def test_should_have_near_zero_RR_genotype_likelihood_for_hom_alt_call(
self):
chr1 = 'chr1'
sample_bank = SampleBank("TTTTTAAAAAAAAAAAAAAAAAAAA", chrom=chr1)
sequence_bank_1 = sample_bank.add_sample_name('sample_1')
sequence_bank_1.add_sequence(".........................",
n_fwd=20,
n_rev=20)
sequence_bank_2 = sample_bank.add_sample_name('sample_2')
sequence_bank_2.add_sequence("............C............",
n_fwd=20,
n_rev=20)
vc_wrapper_builder = VariantCallerBuilderFromSampleBank(
sample_bank, self.work_dir)
variant_output = vc_wrapper_builder.build().run().output_vcf
vcf_expectation = VCFExpectation(self, variant_output)
record_expectation = vcf_expectation.has_record_for_variant(
Variant(chr1, 12, "A", "C"))
sample_expectation = record_expectation.with_sample("sample_1")
sample_expectation.has_genotype("0|0").has_RR_genotype_likelihood(0.0)
def test_should_raise_when_adding_existing_sample(self):
sample_bank = SampleBank("AAA")
sample_name = "SAMPLE1"
sample_bank.add_sample_name(sample_name)
self.assertRaisesRegex(
weCallException,
"Sample SAMPLE1 already exists in the SampleBank.",
sample_bank.add_sample_with_seqs_and_quals, sample_name, [])
def test_should_add_seq_and_quals_list_with_fwd_and_rev_reads(self):
sample_bank = SampleBank("AAA")
sample_bank.add_sample_with_seqs_and_quals("SAMPLE1", ["...", "007"],
n_fwd=1,
n_rev=2)
self.assertEqual(len(sample_bank["SAMPLE1"]), 1)
self.assertEqual(sample_bank["SAMPLE1"][0].n_fwd, 1)
self.assertEqual(sample_bank["SAMPLE1"][0].n_rev, 2)
def test_should_add_short_sequence_and_quality_list(self):
sample_bank = SampleBank("AAA")
sample_bank.add_sample_with_seqs_and_quals("SAMPLE1", ["...", "007"])
read_lists = [
builder.build_reads(0, {}) for builder in sample_bank["SAMPLE1"]
]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].qual, "!!g")
def test_should_add_seq_and_quals_list_with_deletion(self):
sample_bank = SampleBank("AAA")
sample_bank.add_sample_with_seqs_and_quals("SAMPLE1", [".*C", "1 3"])
read_lists = [
builder.build_reads(0, {}) for builder in sample_bank["SAMPLE1"]
]
reads = [read for read_list in read_lists for read in read_list]
self.assertEqual(reads[0].qual, "+?")
def __run_wecall_variant_caller(self, chrom, reference_string, sequence_list, vcf_stem=None):
if vcf_stem is None:
vcf_stem = chrom
sample_bank = SampleBank(reference_string, chrom=chrom)
sample_bank.add_sample_with_seqs_and_quals(DEFAULT_SAMPLE_NAME, sequence_list, n_fwd=10, n_rev=10)
vc_builder = VariantCallerBuilderFromSampleBank(sample_bank, self.work_dir)
vc_wrapper = vc_builder.build()
vc_wrapper.add_additional_command("allowMNPCalls", False)
vc_wrapper.output_vcf = path.join(self.intermediate_vcfs_dir, "{}.vcf".format(vcf_stem))
vc_wrapper.run()
return vc_wrapper.output_vcf
def __build_default_sample_bank(
self,
ref,
sequence_list,
n_fwd=None,
n_rev=None):
sample_bank = SampleBank(ref)
sample_bank.add_sample_with_seqs_and_quals(
DEFAULT_SAMPLE_NAME, sequence_list, n_fwd, n_rev)
return sample_bank
def test_should_add_two_sequence_list(self):
sample_bank = SampleBank("AAA")
sample_bank.add_sample_with_seqs_and_quals("SAMPLE1", ["...", " .."])
read_lists = [
builder.build_reads(0, {}) for builder in sample_bank["SAMPLE1"]
]
reads = [read for read_list in read_lists for read in read_list]
reads.sort(key=lambda x: (x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
self.assertEqual(len(reads), 2)
self.assertEqual(reads[0].qual, "HHH")
self.assertEqual(reads[1].qual, "HH")
def test_should_place_variants_at_custom_position(self):
sample_bank = SampleBank("AAATTTTGGGAG", 100)
sample_bank.add_sample_name("SAMPLE1")
sample_bank.add_sample_name("SAMPLE2")
sample_bank["SAMPLE1"].add_sequence(".....G......")
sample_bank["SAMPLE2"].add_sequence("..........*.")
exp_variant1 = Variant(sample_bank.reference.chrom, 105, "T", "G")
exp_variant2 = Variant(sample_bank.reference.chrom, 109, "GA", "G")
self.assertEqual(sample_bank["SAMPLE1"].variants, {exp_variant1})
self.assertEqual(sample_bank["SAMPLE2"].variants, {exp_variant2})
self.assertEqual(sample_bank.variants, {exp_variant1, exp_variant2})
def test_should_return_all_variants(self):
sample_bank = SampleBank("AAATTTTGGGAG")
sample_bank.add_sample_name("SAMPLE1")
sample_bank.add_sample_name("SAMPLE2")
sample_bank["SAMPLE1"].add_sequence(".....G......")
sample_bank["SAMPLE2"].add_sequence("..........*.")
exp_variant1 = Variant(sample_bank.reference.chrom, 5, "T", "G")
exp_variant2 = Variant(sample_bank.reference.chrom, 9, "GA", "G")
self.assertEqual(sample_bank["SAMPLE1"].variants, {exp_variant1})
self.assertEqual(sample_bank["SAMPLE2"].variants, {exp_variant2})
self.assertEqual(sample_bank.variants, {exp_variant1, exp_variant2})
def test_should_add_sequence_with_quality(self):
sample_bank = SampleBank("AAA")
sample_name = "SAMPLE1"
sample_bank.add_sample_name(sample_name)
sample_bank[sample_name].add_sequence("...", quality_string="007")
read_lists = [
builder.build_reads(0, {}) for builder in sample_bank["SAMPLE1"]
]
reads = [read for read_list in read_lists for read in read_list]
# ascii: "0": "!", "1": "+", "2": "5", "3": "?", "4": "I", "5": "S",
# "6": "]", "7": "g", "8": "q", "9": "{"
self.assertEqual(reads[0].qual, "!!g")
def test_should_add_complex_seq_and_quals_list(self):
sample_bank = SampleBank("AAA")
sample_bank.add_sample_with_seqs_and_quals(
"SAMPLE1", ["...", "007", " ..", ".*C", "1 3"])
read_lists = [
builder.build_reads(0, {}) for builder in sample_bank["SAMPLE1"]
]
reads = [read for read_list in read_lists for read in read_list]
reads.sort(key=lambda x: (x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
self.assertEqual(len(reads), 3)
self.assertEqual(reads[0].qual, "!!g")
self.assertEqual(reads[1].qual, "+?")
self.assertEqual(reads[2].qual, self.default_char * 2)
def test_should_raise_when_multiple_quality_strings_specified_per_sequence(
self):
sample_bank = SampleBank("AAA")
self.assertRaisesRegex(weCallException,
"Illegal character in sequence \'008\'",
sample_bank.add_sample_with_seqs_and_quals,
"SAMPLE1", ["...", "007", "008"])
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_can_build_correct_ref_and_bam_file(self):
bank = SampleBank("ATCCT*ATAATAAATAAATAAT")
sample_name = "TEST_SAMPLE"
bank.add_sample_name(sample_name)
bank[sample_name].add_sequence("....CT.........T......")
builder = WecallInputDataBuilder(self.work_dir).with_sample_bank(bank)
input_files = builder.build()
bam_file = pysam.Samfile(input_files.bam_filenames[0], "rb")
for read in bam_file.fetch():
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "ATCCCTATAATAAATTAATAAT")
self.assertEqual(read.cigarstring, "5M1I16M")
fasta_file = pysam.Fastafile(input_files.reference_filename)
self.assertEqual(fasta_file.get_reference_length(bank.reference.chrom),
21)
self.assertEqual(fasta_file.fetch(bank.reference.chrom, 0, 21),
"ATCCTATAATAAATAAATAAT")
def calls_variants_from_samples(self,
ref,
sample_seqs,
expected_haplotypes=None,
expected_call_stubs=None,
config_dict=None):
"""
:param expected_haplotypes: dictionary: {sample_name : list of two ascii sequences expressing the genotype}
:param expected_call_stubs: dictionary: {variant_stub: dictionary {sample_name: str(genotype)} }
"""
self.__validate_expected_calls(
expected_haplotypes, expected_call_stubs)
sample_bank = SampleBank(ref)
for sample_name, sequence_list in sample_seqs.items():
sample_bank.add_sample_with_seqs_and_quals(
sample_name, sequence_list)
variant_callset = self.__run_wecall(sample_bank, config_dict)
wecall_calls = variant_callset.get_variants_with_genotypes()
if expected_call_stubs is None:
self.__filter_none_genotypes(wecall_calls)
expected_calls = self.__get_expected_calls_from_sample_ascii_haplotypes(
expected_haplotypes, sample_bank.reference)
else:
expected_calls = {}
for variant_stub, genotypes in expected_call_stubs.items():
variant = self._variant_from_stub(
sample_bank.reference.chrom, variant_stub)
expected_calls[variant] = OrderedDict()
for sample_name, genotype in genotypes.items():
expected_calls[variant][sample_name] = GenotypeCall(
genotype)
self.maxDiff = None # print the whole message if the following assertion fails
self.assertDictEqual(expected_calls, wecall_calls)
def assert_quality_recalibrated_in_output_bam(self, ref_string,
input_bam_seqs,
output_bam_seqs):
input_sample_bank = SampleBank(ref_string)
input_sample_bank.add_sample_with_seqs_and_quals(
self.sample_name, input_bam_seqs)
output_sample_bank = SampleBank(ref_string)
output_sample_bank.add_sample_with_seqs_and_quals(
self.sample_name, output_bam_seqs)
vc_builder = VariantCallerBuilderFromSampleBank(
input_sample_bank, self.work_dir)
vc_builder.configuration["recalibrateBaseQs"] = "true"
vc_builder.configuration[
"intermediateRecalibFileStem"] = self.output_stem
vc_builder.build().run()
self.assertTrue(os.path.exists(self.output_sam))
sam_file = pysam.Samfile(self.output_sam, "r")
reads = list(sam_file.fetch())
self.assertEqual(len(reads), len(output_sample_bank[self.sample_name]))
# Sort the sam as in sequence bank.
# output_sample_bank.sort_sequence_banks()
output_reads = sorted(output_sample_bank[self.sample_name].build_reads(
0, {}),
key=lambda x:
(x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
reads.sort(key=lambda x: (x.pos, x.seq, x.qual, x.cigarstring, x.mapq))
for read, expected_sequence in zip(reads, output_reads):
self.assertEqual(read.pos, expected_sequence.pos)
self.assertEqual(read.seq, expected_sequence.seq)
self.assert_matching_ascii_qualities(read.qual,
expected_sequence.qual)
self.assertEqual(read.cigarstring, expected_sequence.cigarstring)
self.assertEqual(read.mapq, expected_sequence.mapq)
sam_file.close()
def test_should_be_able_to_build_bam_and_ref_data_with_multiple_chromosomes(
self):
bank_1 = SampleBank("A" * 10, 0, chrom='10')
bank_1.add_sample_name("sample").add_sequence("." * 10)
bank_2 = SampleBank("T" * 9, 0, chrom='20')
bank_2.add_sample_name("sample").add_sequence("." * 9)
builder = WecallInputDataBuilder(
self.work_dir).with_sample_bank(bank_1).with_sample_bank(bank_2)
input_files = builder.build()
bam_file = pysam.Samfile(input_files.bam_filenames[0], "rb")
for read in bam_file.fetch(reference='20'):
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "T" * 9)
self.assertEqual(read.cigarstring, "9M")
for read in bam_file.fetch(reference='10'):
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "A" * 10)
self.assertEqual(read.cigarstring, "10M")
print((dir(read)))
def test_can_build_multiple_bam_files(self):
bank = SampleBank("ATCCT*ATAATAAATAAATAAT")
sample_name1 = "TEST_SAMPLE1"
bank.add_sample_name(sample_name1)
bank[sample_name1].add_sequence("....CT.........T......")
sample_name2 = "TEST_SAMPLE2"
bank.add_sample_name(sample_name2)
bank[sample_name2].add_sequence(".....*.G..........*...")
builder = WecallInputDataBuilder(self.work_dir).with_sample_bank(bank)
input_bams = builder.build().bam_filenames
bam_file1 = pysam.Samfile(input_bams[0], "rb")
for read in bam_file1.fetch():
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "ATCCCTATAATAAATTAATAAT")
self.assertEqual(read.cigarstring, "5M1I16M")
bam_file2 = pysam.Samfile(input_bams[1], "rb")
for read in bam_file2.fetch():
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "ATCCTAGAATAAATAAAAAT")
self.assertEqual(read.cigarstring, "17M1D3M")
def with_ref_sequence(self, ref_sequence, pos_from=0, chrom=DEFAULT_CHROM):
self._sample_bank[chrom] = SampleBank(ref_sequence, pos_from, chrom)
return self
