parser.add_argument('probanno', help='ID of ProbAnno object', action='store', default=None)
parser.add_argument('-w', '--probannows', help='workspace where ProbAnno object is saved', action='store', dest='probannows', default=None)
parser.add_argument('--genomews', help='workspace where Genome object is saved', action='store', dest='genomews', default=None)
parser.add_argument('--url', help='url for service', action='store', dest='url', default=None)
parser.add_argument('-e', '--show-error', help='show detailed information for an exception', action='store_true', dest='showError', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# 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)
parser.add_argument('probanno', help='ID of ProbAnno object', action='store', default=None)
parser.add_argument('-w', '--workspace', help='workspace where ProbAnno object is saved', action='store', dest='probannows', default=None)
parser.add_argument('-v', '--version', help='version number of ProbAnno object', action='store', dest='probannover', type=int, default=None)
parser.add_argument('-r', '--roles', help='Print role likelihoods instead of annotation likelihoods', action='store_true', dest='roles', default=False)
parser.add_argument('-u', '--url', help='url for service', action='store', dest='url', default=None)
parser.add_argument('-e', '--show-error', help='show detailed information for an exception', action='store_true', dest='showError', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['probanno'] = args.probanno
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
input['probanno_version'] = args.probannover
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_probanno(input)
except Exception as e:
print 'Error getting ProbAnno object: %s' %(e.message)
if args.showError:
parser.add_argument('-e',
'--show-error',
help='show detailed information for an exception',
action='store_true',
dest='showError',
default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['rxnprobs'] = args.rxnprobs
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['rxnprobs_version'] = args.rxnprobsver
input['sort_field'] = args.sortField
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_rxnprobs(input)
except Exception as e:
print 'Error getting RxnProbs object: %s' % (e.message)
parser.add_argument('--probannows', help='workspace where ProbAnno object is stored', action='store', dest='probannows', default=None)
parser.add_argument('-t', '--template', help='ID of ModelTemplate object', action='store', dest='template', default=None)
parser.add_argument('--templatews', help='workspace where ModelTemplate object is stored', action='store', dest='templatews', default=None)
parser.add_argument('--url', help='url for service', action='store', dest='url', default=None)
parser.add_argument('-e', '--show-error', help='show detailed information for an exception', action='store_true', dest='showError', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['probanno'] = args.probanno
input['rxnprobs'] = args.rxnprobs
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['template_model'] = args.template
input['template_workspace'] = args.templatews
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Calculate reaction probabilities from probabilistic annotation.
parser.add_argument('rxnprobs', help='ID of RxnProbs object', action='store', default=None)
parser.add_argument('-w', '--workspace', help='workspace where RxnProbs object is saved', action='store', dest='rxnprobsws', default=None)
parser.add_argument('-v', '--version', help='version number of RxnProbs object', action='store', dest='rxnprobsver', type=int, default=None)
parser.add_argument('--sort', help='field to use as key for sorting output table', action='store', dest='sortField', default='rxnid')
parser.add_argument('-u', '--url', help='url for service', action='store', dest='url', default=None)
parser.add_argument('-e', '--show-error', help='show detailed information for an exception', action='store_true', dest='showError', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['rxnprobs'] = args.rxnprobs
if args.rxnprobsws is None:
input['rxnprobs_workspace'] = user_workspace()
else:
input['rxnprobs_workspace'] = args.rxnprobsws
input['rxnprobs_version'] = args.rxnprobsver
input['sort_field'] = args.sortField
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_rxnprobs(input)
except Exception as e:
print 'Error getting RxnProbs object: %s' %(e.message)
parser.add_argument('-e',
'--show-error',
help='show detailed information for an exception',
action='store_true',
dest='showError',
default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create input parameters for annotate() function.
input = dict()
input['probanno'] = args.probanno
if args.probannows is None:
input['probanno_workspace'] = user_workspace()
else:
input['probanno_workspace'] = args.probannows
input['probanno_version'] = args.probannover
# Create a probabilistic annotation client.
if args.url is None:
args.url = get_url()
paClient = ProbabilisticAnnotation(url=args.url)
# Get the raw data from the server.
try:
output = paClient.get_probanno(input)
except Exception as e:
print 'Error getting ProbAnno object: %s' % (e.message)
if args.showError: