def run(self):
if os.path.exists(self.args.output):
logging.info("%s already exists. Delete it if you want it done again", self.args.output)
return
logging.info("Loading %s", self.args.weight_db)
weight_db_logic = WeightDBUtilities.WeightDBEntryLogic(self.args.weight_db)
logging.info("Loaded %s genes", len(weight_db_logic.gene_data_for_gene))
logging.info("Building snp dict from %s", self.args.gtex_snp)
snp_dict = GTExSNPFile.build_snp_dict(self.args.gtex_snp, weight_db_logic)
logging.info("Got %d snps in dictionary", len(snp_dict))
logging.info("Building gene expression")
gene_expression, individuals = GTExGenoFile.build_gene_expression(self.args.gtex_geno, weight_db_logic, snp_dict)
logging.info("Loaded %d gene expression", len(gene_expression))
if self.args.gencode_file:
logging.info("Translating gene names to ensemble id")
ensemble_to_name, name_to_ensemble = GencodeFile.ensemble_to_name_relationships(self.args.gencode_file)
logging.info("Loaded %d (%d) names", len(ensemble_to_name), len(name_to_ensemble))
keys = gene_expression.keys()
for k in keys:
expression = gene_expression[k]
if k in ensemble_to_name:
pass
elif k in name_to_ensemble:
del gene_expression[k]
ensemble_id = name_to_ensemble[k]
gene_expression[ensemble_id] = expression
else:
del gene_expression[k]
logging.info("Saving gene expression for %d genes", len(gene_expression))
save_expression(self.args.output, gene_expression, individuals)
