def _get_puzzle_variant(self, gemini_variant, index): """Take a gemini variant and return a basic puzzle variant For the overview we only need limited variant information """ variant_dict = { 'CHROM':gemini_variant['chrom'].lstrip('chrCHR'), 'POS':str(gemini_variant['start']), 'ID':gemini_variant['rs_ids'], 'REF':gemini_variant['ref'], 'ALT':gemini_variant['alt'], 'QUAL':gemini_variant['qual'], 'FILTER':gemini_variant['filter'] } variant = Variant(**variant_dict) variant['index'] = index # Use the gemini id for fast search variant.update_variant_id(gemini_variant['variant_id']) #Add the most severe consequence variant['most_severe_consequence'] = gemini_variant['impact_so'] #Add the impact severity variant['impact_severity'] = gemini_variant['impact_severity'] max_freq = gemini_variant['max_aaf_all'] if max_freq: variant.set_max_freq(max_freq) #### Check the impact annotations #### if gemini_variant['cadd_scaled']: variant['cadd_score'] = gemini_variant['cadd_scaled'] return variant
def _format_variant(self, gemini_variant, individual_objs, index=0): """Make a puzzle variant from a gemini variant Args: gemini_variant (GeminiQueryRow): The gemini variant individual_objs (list(dict)): A list of Individuals index(int): The index of the variant Returns: variant (dict): A Variant object """ variant_dict = { 'CHROM':gemini_variant['chrom'].lstrip('chrCHR'), 'POS':str(gemini_variant['start']), 'ID':gemini_variant['rs_ids'], 'REF':gemini_variant['ref'], 'ALT':gemini_variant['alt'], 'QUAL':gemini_variant['qual'], 'FILTER':gemini_variant['filter'] } variant = Variant(**variant_dict) variant['index'] = index # Use the gemini id for fast search variant.update_variant_id(gemini_variant['variant_id']) # Update the individuals individual_genotypes = self._get_genotypes( gemini_variant=gemini_variant, individual_objs=individual_objs ) for individual in individual_genotypes: # Add the genotype calls to the variant variant.add_individual(individual) for transcript in self._get_transcripts(gemini_variant): variant.add_transcript(transcript) #Add the most severe consequence variant['most_severe_consequence'] = gemini_variant['impact_so'] for gene in self._get_genes(variant): variant.add_gene(gene) variant['start'] = int(variant_dict['POS']) if self.variant_type == 'sv': other_chrom = variant['CHROM'] # If we have a translocation: if ':' in variant_dict['ALT']: other_coordinates = variant_dict['ALT'].strip('ACGTN[]').split(':') other_chrom = other_coordinates[0].lstrip('chrCHR') other_position = other_coordinates[1] variant['stop'] = other_position #Set 'infinity' to length if translocation variant['sv_len'] = float('inf') variant['sv_type'] = 'BND' else: variant['stop'] = int(gemini_variant['end']) variant['sv_len'] = variant['stop'] - variant['start'] variant['sv_type'] = gemini_variant['sub_type'] variant['stop_chrom'] = other_chrom else: variant['stop'] = int(variant_dict['POS']) + \ (len(variant_dict['REF']) - len(variant_dict['ALT'])) variant['cytoband_start'] = get_cytoband_coord( chrom=variant['CHROM'], pos=variant['start']) if variant.get('stop_chrom'): variant['cytoband_stop'] = get_cytoband_coord( chrom=variant['stop_chrom'], pos=variant['stop']) #### Check the impact annotations #### if gemini_variant['cadd_scaled']: variant['cadd_score'] = gemini_variant['cadd_scaled'] # We use the prediction in text polyphen = gemini_variant['polyphen_pred'] if polyphen: variant.add_severity('Polyphen', polyphen) # We use the prediction in text sift = gemini_variant['sift_pred'] if sift: variant.add_severity('SIFT', sift) #### Check the frequencies #### thousand_g = gemini_variant['aaf_1kg_all'] if thousand_g: variant['thousand_g'] = float(thousand_g) variant.add_frequency(name='1000GAF', value=float(thousand_g)) exac = gemini_variant['aaf_exac_all'] if exac: variant.add_frequency(name='EXaC', value=float(exac)) esp = gemini_variant['aaf_esp_all'] if esp: variant.add_frequency(name='ESP', value=float(esp)) max_freq = gemini_variant['max_aaf_all'] if max_freq: variant.set_max_freq(max_freq) return variant
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