def run_additional(args, context):
logging.info("Started metaxcan additional stats")
i_genes, i_snps = context.get_data_intersection()
results = []
for gene in i_genes:
stats_ = AssociationCalculation.additional_stats(gene, context)
results.append(stats_)
results = AssociationCalculation.dataframe_from_aditional_stats(results)
results = MetaxcanUtilities.format_additional_output(results, context, args.remove_ens_version)
if args.additional_output:
Utilities.ensure_requisite_folders(args.additional_output)
results.to_csv(args.additional_output, index=False)
return results
def run_metaxcan(args, context):
logging.info("Started metaxcan association")
model_snps = context.get_model_snps()
total_snps = len(model_snps)
snps_found = set()
reporter = Utilities.PercentReporter(logging.INFO, total_snps)
i_genes, i_snps = context.get_data_intersection()
results = []
additional = []
for i, gene in enumerate(i_genes):
if args.MAX_R and i + 1 > args.MAX_R:
logging.log("Early exit condition met")
break
logging.log(9, "Processing gene %i:%s", i, gene)
r, snps = AssociationCalculation.association(gene,
context,
return_snps=True)
results.append(r)
snps_found.update(snps)
reporter.update(
len(snps_found),
"%d %% of model's snps found so far in the gwas study")
if args.additional_output:
stats_ = AssociationCalculation.additional_stats(gene, context)
additional.append(stats_)
reporter.update(len(snps_found), "%d %% of model's snps used", force=True)
results = AssociationCalculation.dataframe_from_results(results)
results = MetaxcanUtilities.format_output(results, context,
args.remove_ens_version)
if args.additional_output:
additional = AssociationCalculation.dataframe_from_aditional_stats(
additional)
results = MetaxcanUtilities.merge_additional_output(
results, additional, context, args.remove_ens_version)
if args.output_file:
Utilities.ensure_requisite_folders(args.output_file)
results.to_csv(args.output_file, index=False)
return results