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 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 __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_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 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 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 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)