def test_get_probanno(self):
''' Verify that we can successfully get a list of roleset probabilities from a valid ProbAnno object. '''
paClient = ProbabilisticAnnotation(self._config["probanno_url"], token=self._token)
probAnnoData = paClient.get_probanno( {
"probanno": self._config["probannoid"],
"probanno_workspace": self._config["test_ws"]
})
self.assertNotEqual(len(probAnnoData), 0, 'Length of output array is zero')
def test_get_probanno(self):
''' Verify that we can successfully get a list of roleset probabilities from a valid ProbAnno object. '''
paClient = ProbabilisticAnnotation(self._config["probanno_url"],
token=self._token)
probAnnoData = paClient.get_probanno({
"probanno":
self._config["probannoid"],
"probanno_workspace":
self._config["test_ws"]
})
self.assertNotEqual(len(probAnnoData), 0,
'Length of output array is zero')
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:
traceback.print_exc(file=sys.stdout)
exit(1)
# Format the data as a table of tab delimited fields.
if args.roles:
print '\t'.join(['gene', 'role', 'likelihood'])
else:
print '\t'.join(['gene', 'annotation', 'likelihood'])
for gene in output:
roleToProb = dict()
for roleprob in output[gene]:
if args.roles:
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:
traceback.print_exc(file=sys.stdout)
exit(1)
# Format the data as a table of tab delimited fields.
if args.roles:
print '\t'.join(['gene', 'role', 'likelihood'])
else:
print '\t'.join(['gene', 'annotation', 'likelihood'])
for gene in output:
roleToProb = dict()
for roleprob in output[gene]:
if args.roles:
