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)
