# Create input parameters for annotate() function.
input = dict()
input['genome'] = args.genome
input['probanno'] = args.probanno
if args.genomews is None:
input['genome_workspace'] = user_workspace()
else:
input['genome_workspace'] = args.genomews
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Submit a job to annotate the specified genome.
try:
jobid = paClient.annotate(input)
print 'Probabilistic annotation job '+jobid+' successfully submitted'
except Exception as e:
print 'Error starting job: %s' %(e.message)
if args.showError:
traceback.print_exc(file=sys.stdout)
exit(1)
exit(0)
SEE ALSO
pa-gendata
AUTHORS
Matt Benedict, Mike Mundy
'''
# Main script function
if __name__ == "__main__":
# Parse arguments.
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog='pa-savedata', epilog=desc3)
parser.add_argument('configFilePath', help='path to configuration file', action='store', default=None)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Get the probabilistic_annotation section from the configuration file.
config = get_config(args.configFilePath)
# Create a DataParser object for working with the static database files.
dataParser = DataParser(config)
# Store the static database files in Shock.
paClient = ProbabilisticAnnotation(url=get_url())
dataParser.storeDatabaseFiles(paClient._headers['AUTHORIZATION'])
exit(0)
'''
# Main script function
if __name__ == "__main__":
# Parse arguments.
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
prog='pa-savedata',
epilog=desc3)
parser.add_argument('configFilePath',
help='path to configuration file',
action='store',
default=None)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Get the probabilistic_annotation section from the configuration file.
config = get_config(args.configFilePath)
# Create a DataParser object for working with the static database files.
dataParser = DataParser(config)
# Store the static database files in Shock.
paClient = ProbabilisticAnnotation(url=get_url())
dataParser.storeDatabaseFiles(paClient._headers['AUTHORIZATION'])
exit(0)
parser.add_argument('newurl',
nargs='?',
default=None,
help='New URL endpoint')
parser.add_argument('--no-check',
help='do not check for a valid URL',
action='store_true',
dest='noCheck',
default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
if args.newurl == None:
url = get_url()
print "Current URL: " + url
else:
url = set_url(args.newurl)
if args.noCheck:
print 'New URL set to: ' + url
exit(0)
try:
paClient = ProbabilisticAnnotation(url=url)
serverInfo = paClient.version()
if serverInfo[0] != 'probabilistic_annotation':
print url + ' is not a probabilistic annotation server'
exit(1)
print url + ' is valid and running %s v%s' % (serverInfo[0],
serverInfo[1])
except ProbAnnoServerError as e:
Matt Benedict, Mike Mundy
"""
if __name__ == "__main__":
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog="pa_url", epilog=desc3)
parser.add_argument("newurl", nargs="?", default=None, help="New URL endpoint")
parser.add_argument(
"--no-check", help="do not check for a valid URL", action="store_true", dest="noCheck", default=False
)
usage = parser.format_usage()
parser.description = desc1 + " " + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
if args.newurl == None:
url = get_url()
print "Current URL: " + url
else:
url = set_url(args.newurl)
if args.noCheck:
print "New URL set to: " + url
exit(0)
try:
paClient = ProbabilisticAnnotation(url=url)
serverInfo = paClient.version()
if serverInfo[0] != "probabilistic_annotation":
print url + " is not a probabilistic annotation server"
exit(1)
print url + " is valid and running %s v%s" % (serverInfo[0], serverInfo[1])
except ProbAnnoServerError as e:
print "Endpoint at %s returned error: %s" % (url, e)
