def get_phenotypes(self,
gene,
diplotypes,
sample_variants,
uncallable,
extra_variants=None):
g = gene.name
# Load phenotype file into object
phenotypes = Phenotype()
results = []
for sample, diplotype in diplotypes.items():
haps = split_genotype(diplotype)
haplotype_data = {}
for i in range(len(haps)):
h = haps[i]
h_function = phenotypes.get_haplotype_function(g, h)
h_presumptive = phenotypes.get_presumptive_haplotype_function(
g, h)
haplotype_data["hap_%s" % i] = h
haplotype_data["hap_%s_function" % i] = h_function
haplotype_data["hap_%s_presumptive" % i] = h_presumptive
phenotype = phenotypes.get_diplotype_function(g, haps[0], haps[1])
presumptive_phenotype = phenotypes.get_diplotype_function(
g, haps[0], haps[1], presumptive=True)
activity_score = phenotypes.get_activity_score(g,
haps[0],
haps[1],
presumptive=True)
#if phenotype != presumptive_phenotype:
# print(phenotype, presumptive_phenotype)
# exit()
results.append({
"sample":
sample,
"gene":
g,
"diplotype":
diplotype,
"hap_1":
haplotype_data["hap_0"],
"hap_2":
haplotype_data["hap_1"],
"hap_1_function":
haplotype_data["hap_0_function"],
"hap_2_function":
haplotype_data["hap_1_function"],
"hap_1_presumptive_function":
haplotype_data["hap_0_presumptive"],
"hap_2_presumptive_function":
haplotype_data["hap_1_presumptive"],
"hap_1_variants":
sample_variants[sample][0],
"hap_2_variants":
sample_variants[sample][1],
"phenotype":
phenotype,
"phenotype_presumptive":
presumptive_phenotype,
"activity_score":
activity_score,
"uncallable":
";".join(x.split("%")[0] for x in uncallable[sample]),
"extra_variants":
None if extra_variants is None else ";".join(
x.split("%")[0] for x in extra_variants[sample])
})
return results
