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())
Exemplo n.º 2
0
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)
Exemplo n.º 3
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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)
Exemplo n.º 4
0
def main():
    args = parseCommandLine()
    phenotypeIdsByName = readPhenotypes(args.hpo)
    lovdPhenotypes = retrieveLovdPhenotypes(args.tsv)
    generateBashScripts(phenotypeIdsByName, lovdPhenotypes, args.out,
                        args.runLimit)