def main():
args = parseCommandLine()
phenotypeIdsByName = readPhenotypes(args.hpo)
lovdPhenotypes = retrieveLovdPhenotypes(args.tsv)
pwd = getpass("Phenotips password for " + args.username + ":")
uploadPhenotypes(args.url, args.username, pwd, lovdPhenotypes, phenotypeIdsByName)
downloadGenes(args.url, args.username, pwd, args.out, lovdPhenotypes.keys())
def main():
# Checks if query_phenomizer is available and exits if not.
validateProgram("query_phenomizer")
args = parseCommandLine()
phenotypeIdsByName = readPhenotypes(args.hpo)
lovdPhenotypes = retrieveLovdPhenotypes(args.tsv)
lovdPhenotypes = convertPhenotypeNamesToIds(lovdPhenotypes, phenotypeIdsByName)
pwd = getpass("Phenomizer password for " + args.username + ":")
retrievePhenomizerResults(lovdPhenotypes, args.username, pwd, args.out)
def main():
# Disables InsecureRequestWarning. See also: https://urllib3.readthedocs.org/en/latest/security.html
disable_warnings(InsecureRequestWarning)
# Runs application processes.
args = parseCommandLine()
phenotypeIdsByName = readPhenotypes(args.hpo)
lovdPhenotypes = retrieveLovdPhenotypes(args.tsv)
lovdPhenotypes = convertPhenotypeNamesToIds(lovdPhenotypes, phenotypeIdsByName)
retrieveGeneNetworkResults(lovdPhenotypes, args.out)
def main():
# Runs application processes.
args = parseCommandLine()
phenotypeIdsByName = readPhenotypes(args.hpo)
convertBenchmarkFile(args.tsv, args.out, phenotypeIdsByName)
def main():
args = parseCommandLine()
phenotypeIdsByName = readPhenotypes(args.hpo)
lovdPhenotypes = retrieveLovdPhenotypes(args.tsv)
generateBashScripts(phenotypeIdsByName, lovdPhenotypes, args.out,
args.runLimit)