def test_mutant_amino_acids_in_mm10_chrX_8125624_refC_altA_pS460I(): # there are two co-occurring variants in the RNAseq data but since # they don't happen in the same codon then we're considering the Varcode # annotation to be correct # TODO: deal with phasing of variants explicitly so that both # variant positions are considered mutated parser = make_protein_sequences_arg_parser() args = parser.parse_args([ "--vcf", data_path("data/b16.f10/b16.f10.Wdr13.vcf"), "--bam", data_path("data/b16.f10/b16.combined.sorted.bam"), "--max-protein-sequences-per-variant", "1", "--protein-sequence-length", "15" ]) for variant, protein_sequences in protein_sequences_generator_from_args(args): protein_sequence = protein_sequences[0] check_mutant_amino_acids(variant, protein_sequence)
def test_mutant_amino_acids_in_mm10_chr9_82927102_refG_altT_pT441H(): # the variant chr9:82927102 G>T occurs right next to T>G so the varcode # prediction for the protein sequence (Asparagine) will be wrong since # the correct translation is Histidine parser = make_protein_sequences_arg_parser() args = parser.parse_args([ "--vcf", data_path("data/b16.f10/b16.f10.Phip.vcf"), "--bam", data_path("data/b16.f10/b16.combined.sorted.bam"), "--max-protein-sequences-per-variant", "1", "--protein-sequence-length", "15" ]) for variant, protein_sequences in protein_sequences_generator_from_args(args): protein_sequence = protein_sequences[0] check_mutant_amino_acids( variant, protein_sequence, expected_amino_acids="H")
def test_mutant_amino_acids_in_mm10_chr9_82927102_refG_altT_pT441H(): # the variant chr9:82927102 G>T occurs right next to T>G so the varcode # prediction for the protein sequence (Asparagine) will be wrong since # the correct translation is Histidine parser = make_protein_sequences_arg_parser() args = parser.parse_args([ "--vcf", data_path("data/b16.f10/b16.f10.Phip.vcf"), "--bam", data_path("data/b16.f10/b16.combined.sorted.bam"), "--max-protein-sequences-per-variant", "1", "--protein-sequence-length", "15" ]) for variant, protein_sequences in protein_sequences_generator_from_args( args): protein_sequence = protein_sequences[0] check_mutant_amino_acids(variant, protein_sequence, expected_amino_acids="H")
def test_mutant_amino_acids_in_mm10_chrX_8125624_refC_altA_pS460I(): # there are two co-occurring variants in the RNAseq data but since # they don't happen in the same codon then we're considering the Varcode # annotation to be correct # TODO: deal with phasing of variants explicitly so that both # variant positions are considered mutated parser = make_protein_sequences_arg_parser() args = parser.parse_args([ "--vcf", data_path("data/b16.f10/b16.f10.Wdr13.vcf"), "--bam", data_path("data/b16.f10/b16.combined.sorted.bam"), "--max-protein-sequences-per-variant", "1", "--protein-sequence-length", "15" ]) for variant, protein_sequences in protein_sequences_generator_from_args( args): protein_sequence = protein_sequences[0] check_mutant_amino_acids(variant, protein_sequence)