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_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 __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_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_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_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_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_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 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")