def _format_variants(self, variant, index, case_obj, add_all_info=False): """Return a Variant object Format variant make a variant that includes enough information for the variant view. If add_all_info then all transcripts will be parsed Args: variant (cython2.Variant): A variant object index (int): The index of the variant case_obj (puzzle.models.Case): A case object """ header_line = self.head.header # Get the individual ids for individuals in vcf file vcf_individuals = set([ind_id for ind_id in self.head.individuals]) #Create a info dict: info_dict = dict(variant.INFO) chrom = variant.CHROM if chrom.startswith('chr') or chrom.startswith('CHR'): chrom = chrom[3:] variant_obj = Variant( CHROM=chrom, POS=variant.POS, ID=variant.ID, REF=variant.REF, ALT=variant.ALT[0], QUAL=variant.QUAL, FILTER=variant.FILTER, ) variant_obj._set_variant_id() logger.debug("Creating a variant object of variant {0}".format( variant_obj.variant_id)) variant_obj.index = index logger.debug("Updating index to: {0}".format(index)) ########### Get the coordinates for the variant ############## variant_obj.start = variant.start variant_obj.stop = variant.end #SV variants needs to be handeled a bit different since the can be huge #it would take to much power to parse all vep/snpeff entrys for these. if self.variant_type == 'sv': variant_obj.stop = int(info_dict.get('END', variant_obj.POS)) self._add_sv_coordinates(variant_obj) variant_obj.sv_type = info_dict.get('SVTYPE') # Special for FindSV software: # SV specific tag for number of occurances occurances = info_dict.get('OCC') if occurances: logger.debug("Updating occurances to: {0}".format(occurances)) variant_obj['occurances'] = float(occurances) variant_obj.add_frequency('OCC', occurances) else: self._add_thousand_g(variant_obj, info_dict) self._add_cadd_score(variant_obj, info_dict) self._add_genetic_models(variant_obj, info_dict) self._add_transcripts(variant_obj, info_dict) self._add_exac(variant_obj, info_dict) self._add_hgnc_symbols(variant_obj) if add_all_info: self._add_genotype_calls(variant_obj, str(variant), case_obj) self._add_compounds(variant_obj, info_dict) self._add_gmaf(variant_obj, info_dict) self._add_genes(variant_obj) ##### Add consequences #### self._add_consequences(variant_obj, str(variant)) self._add_most_severe_consequence(variant_obj) self._add_impact_severity(variant_obj) self._add_rank_score(variant_obj, info_dict) variant_obj.set_max_freq() return variant_obj