def save_study(study, selected_snps, simulated_gencode, prefix, _save):
Utilities.ensure_requisite_folders(prefix)
_save(study)
selected_snps_ = prefix + ".selected_snps.txt.gz"
Utilities.write_iterable_to_file(selected_snps, selected_snps_)
gencode_path = os.path.join(os.path.split(prefix)[0], "gene_annotation.txt.gz")
Utilities.save_dataframe(simulated_gencode, gencode_path)
def run(args):
if os.path.exists(args.output):
logging.info("Output exists. Nope.")
return
logging.info("Loading samples")
samples = {x for x in TextFileTools.load_list(args.samples_whitelist)}
logging.info("Processing file")
Utilities.ensure_requisite_folders(args.output)
Utilities.write_iterable_to_file(input_generator(args.input_file, samples), args.output)
logging.info("Finished")
def run(args):
if (not args.output
and not args.output_blacklist) or (args.output
and args.output_blacklist):
logging.info("Provide only one output argument")
return
if args.output and os.path.exists(args.output):
logging.info("Output path %s exists. Nope.", args.output)
return
if args.output_blacklist and os.path.exists(args.output_blacklist):
logging.info("Output path for skipped variants %s exists. Nope.",
args.output_blacklist)
return
start = timer()
logging.info("Started parsing DB SNP file")
if args.output:
Utilities.ensure_requisite_folders(args.output)
entries = Utilities.lineify(
DBSnp.generate(args.input,
args.fields,
args.keep_zero_based,
recode_observed=args.recode_observed))
Utilities.write_iterable_to_file(entries, args.output,
Utilities.to_line(args.fields))
else:
Utilities.ensure_requisite_folders(args.output_blacklist)
entries = Utilities.lineify(
DBSnp.generate_skips(args.input,
args.fields,
args.keep_zero_based,
recode_observed=args.recode_observed))
Utilities.write_iterable_to_file(
entries, args.output_blacklist,
Utilities.to_line(args.fields + ["reason"]))
end = timer()
logging.info("Finished parsing at %s", str(end - start))
def run(args):
delim = args.delimiter
out_delim = delim if delim else "\t"
Utilities.write_iterable_to_file(
_get_lines(args.input_file, args.columns, delim, out_delim),
args.output_file)
