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,
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