def initializeMutFromAttributes(chr, start, end, ref_allele, alt_allele, build, mutation_data_factory=None):
mutation_data_factory = MutationDataFactory() if mutation_data_factory is None else mutation_data_factory
mut = mutation_data_factory.create(str(chr), str(start), str(end), ref_allele, alt_allele, str(build))
varType = TranscriptProviderUtils.infer_variant_type(mut.ref_allele, mut.alt_allele)
if TranscriptProviderUtils.is_xnp(varType): # Snps and other xNPs
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue="")
if varType == VariantClassification.VT_DEL: # deletion
preceding_bases, updated_ref_allele, updated_start, updated_end =\
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut["ref_allele"] = updated_ref_allele
mut.alt_allele = "-"
mut["alt_allele"] = "-"
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
elif varType == VariantClassification.VT_INS: # insertion
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut["ref_allele"] = "-"
mut.alt_allele = updated_alt_allele
mut["alt_allele"] = updated_alt_allele
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
return mut
def _add(self, mutation):
variant_type = TranscriptProviderUtils.infer_variant_type(mutation.ref_allele, mutation.alt_allele)
# only combine ONPs, not indels
if not TranscriptProviderUtils.is_xnp(variant_type):
self.indel_queue.append(mutation)
else:
self.queue[self.sns.getSampleName(mutation)].append(mutation)
def initializeMutFromAttributes(chr, start, end, ref_allele, alt_allele, build):
mut = MutationData(str(chr), str(start), str(end), ref_allele, alt_allele, str(build))
varType = TranscriptProviderUtils.infer_variant_type(mut.ref_allele, mut.alt_allele)
if TranscriptProviderUtils.is_xnp(varType): # Snps and other xNPs
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue="")
if varType == VariantClassification.VT_DEL: # deletion
preceding_bases, updated_ref_allele, updated_start, updated_end =\
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut["ref_allele"] = updated_ref_allele
mut.alt_allele = "-"
mut["alt_allele"] = "-"
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
elif varType == VariantClassification.VT_INS: # insertion
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut["ref_allele"] = "-"
mut.alt_allele = updated_alt_allele
mut["alt_allele"] = updated_alt_allele
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
return mut
def _add(self, mutation):
variant_type = TranscriptProviderUtils.infer_variant_type(
mutation.ref_allele, mutation.alt_allele)
# only combine ONPs, not indels
if not TranscriptProviderUtils.is_xnp(variant_type):
self.indel_queue.append(mutation)
else:
self.queue[self.sns.getSampleName(mutation)].append(mutation)
