def _format_variant(self, gemini_variant, individual_objs, index=0,
add_all_info=False):
"""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
"""
chrom = gemini_variant['chrom']
if chrom.startswith('chr') or chrom.startswith('CHR'):
chrom = chrom[3:]
variant_dict = {
'CHROM':chrom,
'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)
# Use the gemini id for fast search
variant.update_variant_id(gemini_variant['variant_id'])
logger.debug("Creating a variant object of variant {0}".format(
variant.variant_id))
variant['index'] = index
# Add the most severe consequence
self._add_most_severe_consequence(variant, gemini_variant)
#Add the impact severity
self._add_impact_severity(variant, gemini_variant)
### POSITON ANNOATTIONS ###
variant.start = int(gemini_variant['start'])
variant.stop = int(gemini_variant['end'])
#Add the sv specific coordinates
if self.variant_type == 'sv':
variant.sv_type = gemini_variant['sub_type']
variant.stop = int(gemini_variant['end'])
self._add_sv_coordinates(variant)
else:
### Consequence and region annotations
#Add the transcript information
self._add_transcripts(variant, gemini_variant)
self._add_thousand_g(variant, gemini_variant)
self._add_exac(variant, gemini_variant)
self._add_gmaf(variant, gemini_variant)
#### 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)
#Add the genes based on the hgnc symbols
self._add_hgnc_symbols(variant)
if self.variant_type == 'snv':
self._add_genes(variant)
self._add_consequences(variant)
### GENOTYPE ANNOATTIONS ###
#Get the genotype info
if add_all_info:
self._add_genotypes(variant, gemini_variant, individual_objs)
if self.variant_type == 'sv':
self._add_genes(variant)
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_variant(self,
case_id,
gemini_variant,
individual_objs,
index=0,
add_all_info=False):
"""Make a puzzle variant from a gemini variant
Args:
case_id (str): related case id
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
"""
chrom = gemini_variant['chrom']
if chrom.startswith('chr') or chrom.startswith('CHR'):
chrom = chrom[3:]
variant_dict = {
'CHROM': chrom,
'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)
# Use the gemini id for fast search
variant.update_variant_id(gemini_variant['variant_id'])
logger.debug("Creating a variant object of variant {0}".format(
variant.variant_id))
variant['index'] = index
# Add the most severe consequence
self._add_most_severe_consequence(variant, gemini_variant)
#Add the impact severity
self._add_impact_severity(variant, gemini_variant)
### POSITON ANNOATTIONS ###
variant.start = int(gemini_variant['start'])
variant.stop = int(gemini_variant['end'])
#Add the sv specific coordinates
if self.variant_type == 'sv':
variant.sv_type = gemini_variant['sub_type']
variant.stop = int(gemini_variant['end'])
self._add_sv_coordinates(variant)
else:
### Consequence and region annotations
#Add the transcript information
self._add_transcripts(variant, gemini_variant)
self._add_thousand_g(variant, gemini_variant)
self._add_exac(variant, gemini_variant)
self._add_gmaf(variant, gemini_variant)
#### 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)
#Add the genes based on the hgnc symbols
self._add_hgnc_symbols(variant)
if self.variant_type == 'snv':
self._add_genes(variant)
self._add_consequences(variant)
### GENOTYPE ANNOATTIONS ###
#Get the genotype info
if add_all_info:
self._add_genotypes(variant, gemini_variant, case_id,
individual_objs)
if self.variant_type == 'sv':
self._add_genes(variant)
return variant
