def _add_genotype_calls(self, variant_obj, variant_line, case_obj):
"""Add the genotype calls for the variant
Args:
variant_obj (puzzle.models.Variant)
variant_dict (dict): A variant dictionary
case_obj (puzzle.models.Case)
"""
variant_line = variant_line.split('\t')
#if there is gt calls we have no individuals to add
if len(variant_line) > 8:
gt_format = variant_line[8].split(':')
for individual in case_obj.individuals:
sample_id = individual.ind_id
index = individual.ind_index
gt_call = variant_line[9 + index].split(':')
raw_call = dict(zip(gt_format, gt_call))
genotype = Genotype(**raw_call)
variant_obj.add_individual(
puzzle_genotype(
sample_id=sample_id,
genotype=genotype.genotype,
case_id=case_obj.name,
phenotype=individual.phenotype,
ref_depth=genotype.ref_depth,
alt_depth=genotype.alt_depth,
genotype_quality=genotype.genotype_quality,
depth=genotype.depth_of_coverage,
supporting_evidence=genotype.supporting_evidence,
pe_support=genotype.pe_support,
sr_support=genotype.sr_support,
))
def _add_genotype_calls(self, variant_obj, variant_line, case_obj):
"""Add the genotype calls for the variant
Args:
variant_obj (puzzle.models.Variant)
variant_dict (dict): A variant dictionary
case_obj (puzzle.models.Case)
"""
variant_line = variant_line.split('\t')
#if there is gt calls we have no individuals to add
if len(variant_line) > 8:
gt_format = variant_line[8].split(':')
for individual in case_obj.individuals:
sample_id = individual.ind_id
index = individual.ind_index
gt_call = variant_line[9+index].split(':')
raw_call = dict(zip(gt_format, gt_call))
genotype = Genotype(**raw_call)
variant_obj.add_individual(puzzle_genotype(
sample_id = sample_id,
genotype = genotype.genotype,
case_id = case_obj.name,
phenotype = individual.phenotype,
ref_depth = genotype.ref_depth,
alt_depth = genotype.alt_depth,
genotype_quality = genotype.genotype_quality,
depth = genotype.depth_of_coverage,
supporting_evidence = genotype.supporting_evidence,
pe_support = genotype.pe_support,
sr_support = genotype.sr_support,
))
def _format_variant(self, variant_line, index, case_obj, head):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER']
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
#Create a variant dict:
variant_dict = get_variant_dict(
variant_line = variant_line,
header_line = header_line
)
variant_dict['CHROM'] = variant_dict['CHROM'].lstrip('chrCHR')
#Crreate a info dict:
info_dict = get_info_dict(
info_line = variant_dict['INFO']
)
#Check if vep annotation:
vep_string = info_dict.get('CSQ')
#Check if snpeff annotation:
snpeff_string = info_dict.get('ANN')
if vep_string:
#Get the vep annotations
vep_info = get_vep_info(
vep_string = vep_string,
vep_header = vep_header
)
elif snpeff_string:
#Get the vep annotations
snpeff_info = get_snpeff_info(
snpeff_string = snpeff_string,
snpeff_header = snpeff_header
)
variant = Variant(
**{column: variant_dict.get(column, '.')
for column in variant_columns}
)
logger.debug("Creating a variant object of variant {0}".format(
variant.get('variant_id')))
variant['index'] = index
logger.debug("Updating index to: {0}".format(
index))
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'] and not '<' 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')
else:
variant['stop'] = int(info_dict.get('END', variant_dict['POS']))
variant['sv_len'] = variant['stop'] - variant['start']
variant['stop_chrom'] = other_chrom
else:
variant['stop'] = int(variant_dict['POS']) + \
(len(variant_dict['REF']) - len(variant_dict['ALT']))
variant['sv_type'] = info_dict.get('SVTYPE')
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'])
# It would be easy to update these keys...
thousand_g = info_dict.get('1000GAF')
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(
thousand_g))
variant['thousand_g'] = float(thousand_g)
variant.add_frequency('1000GAF', variant.get('thousand_g'))
#SV specific tag for number of occurances
occurances = info_dict.get('OCC')
if occurances:
logger.debug("Updating occurances to: {0}".format(
occurances))
variant['occurances'] = float(occurances)
variant.add_frequency('OCC', occurances)
cadd_score = info_dict.get('CADD')
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(
cadd_score))
variant['cadd_score'] = float(cadd_score)
rank_score_entry = info_dict.get('RankScore')
if rank_score_entry:
for family_annotation in rank_score_entry.split(','):
rank_score = family_annotation.split(':')[-1]
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['rank_score'] = float(rank_score)
genetic_models_entry = info_dict.get('GeneticModels')
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(','):
for genetic_model in family_annotation.split(':')[-1].split('|'):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['genetic_models'] = genetic_models
#Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(
variant_dict['FORMAT'].split(':'),
variant_dict[sample_id].split(':'))
)
genotype = Genotype(**raw_call)
variant.add_individual(puzzle_genotype(
sample_id = sample_id,
genotype = genotype.genotype,
case_id = individual.case_name,
phenotype = individual.phenotype,
ref_depth = genotype.ref_depth,
alt_depth = genotype.alt_depth,
genotype_quality = genotype.genotype_quality,
depth = genotype.depth_of_coverage,
supporting_evidence = genotype.supporting_evidence,
pe_support = genotype.pe_support,
sr_support = genotype.sr_support,
))
# Add transcript information:
gmaf = None
if vep_string:
for transcript_info in vep_info:
transcript = self._get_vep_transcripts(transcript_info)
gmaf_raw = transcript_info.get('GMAF')
if gmaf_raw:
gmaf = float(gmaf_raw.split(':')[-1])
variant.add_transcript(transcript)
if gmaf:
variant.add_frequency('GMAF', gmaf)
if not variant.thousand_g:
variant.thousand_g = gmaf
elif snpeff_string:
for transcript_info in snpeff_info:
transcript = self._get_snpeff_transcripts(transcript_info)
variant.add_transcript(transcript)
most_severe_consequence = get_most_severe_consequence(
variant['transcripts']
)
if most_severe_consequence:
variant['most_severe_consequence'] = most_severe_consequence
variant['impact_severity'] = IMPACT_SEVERITIES.get(most_severe_consequence)
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
return variant