def determineOtherOptions(args):
opts = dict()
opts[OptionConstants.NO_PREPEND] = not args.prepend
opts[OptionConstants.VCF_OUT_INFER_GENOTYPES] = MutUtils.str2bool(
args.infer_genotypes)
opts[OptionConstants.INFER_ONPS] = args.infer_onps
opts[
OptionConstants.CUSTOM_CANONICAL_TX_LIST_FILE] = args.canonical_tx_file
return opts
def determineOtherOptions(args, logger):
opts = dict()
opts[OptionConstants.NO_PREPEND] = not args.prepend
opts[OptionConstants.VCF_OUT_INFER_GENOTYPES] = MutUtils.str2bool(args.infer_genotypes)
if args.input_format == "VCF" and args.output_format == "VCF":
if opts[OptionConstants.VCF_OUT_INFER_GENOTYPES]:
logger.warn("Infer genotypes option has been set to true. "
"Because the input is a VCF file, infer genotypes will have no effect on the output.")
return opts
def determineOtherOptions(args):
opts = dict()
opts[OptionConstants.NO_PREPEND] = not args.prepend
opts[OptionConstants.VCF_OUT_INFER_GENOTYPES] = MutUtils.str2bool(args.infer_genotypes)
opts[OptionConstants.INFER_ONPS] = args.infer_onps
opts[OptionConstants.CUSTOM_CANONICAL_TX_LIST_FILE] = args.canonical_tx_file
opts[OptionConstants.COLLAPSE_FILTER_COLS] = args.collapse_filter_cols
opts[OptionConstants.REANNOTATE_TCGA_MAF_COLS] = args.reannotate_tcga_maf_cols
opts[OptionConstants.ALLOW_ANNOTATION_OVERWRITING] = args.allow_overwriting
opts[OptionConstants.COLLAPSE_NUMBER_ANNOTATIONS] = args.collapse_number_annotations
return opts
def testGenotypeFieldIsHonored(self):
"""
Tests that no issues arise with genotype values >1 when multiple variants appear on one line.
"""
inputFilename = os.path.join(*["testdata", "vcf", "example.severalGTs.vcf"])
creator = VcfInputMutationCreator(inputFilename)
muts = creator.createMutations()
ctr = 0
for mut in muts:
if MutUtils.str2bool(mut["alt_allele_seen"]):
self.assertTrue(mut['sample_name'] != "NA 00001")
ctr += 1
self.assertTrue(ctr == 7,
str(ctr) + " mutations with alt seen, but expected 7. './.' should not show as a variant.")
def determineOtherOptions(args):
opts = dict()
opts[OptionConstants.NO_PREPEND] = not args.prepend
opts[OptionConstants.VCF_OUT_INFER_GENOTYPES] = MutUtils.str2bool(
args.infer_genotypes)
opts[OptionConstants.INFER_ONPS] = args.infer_onps
opts[
OptionConstants.CUSTOM_CANONICAL_TX_LIST_FILE] = args.canonical_tx_file
opts[OptionConstants.COLLAPSE_FILTER_COLS] = args.collapse_filter_cols
opts[OptionConstants.
REANNOTATE_TCGA_MAF_COLS] = args.reannotate_tcga_maf_cols
opts[OptionConstants.ALLOW_ANNOTATION_OVERWRITING] = args.allow_overwriting
opts[OptionConstants.
COLLAPSE_NUMBER_ANNOTATIONS] = args.collapse_number_annotations
return opts
def determineOtherOptions(args):
opts = dict()
opts[OptionConstants.NO_PREPEND] = not args.prepend
opts[OptionConstants.VCF_OUT_INFER_GENOTYPES] = MutUtils.str2bool(args.infer_genotypes)
return opts
