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)