def load(self, dictionary):
ConfigObject.load(self, dictionary)
#Detect if user provides the data or not
start = 0
if 'start' in dictionary:
start = float(dictionary['start'])
if 'data' not in dictionary:
if 'p' not in dictionary:
raise ParseException(
'Probability is missing in RepeatLengthDistribution'
)
p = float(dictionary['p'])
if 'fractions' not in dictionary:
raise ParseException(
'Fractions are missing in RepeatLengthDistribution'
)
fractions = dictionary['fractions']
self.setParams(p, start, fractions)
else:
data = dictionary['data']
if 'fractionssize' not in dictionary:
raise ParseException(
'Number of fractions is missing in RepeatLengthDistribution'
)
self.train(data, int(dictionary['fractionssize']), start)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "emission" not in dictionary:
raise ParseException("Emission not found in state")
if "name" not in dictionary:
raise ParseException("Name not found in state")
if "startprob" not in dictionary:
raise ParseException("startprob not found in state")
if "endprob" not in dictionary:
raise ParseException("endprob not found in state")
if "serialize" in dictionary:
self.serialize = dictionary["serialize"]
self.stateName = dictionary["name"]
if "onechar" in dictionary:
if len(dictionary['onechar']) != 1:
raise ParseException('onechar has wrong length')
self.onechar = dictionary["onechar"]
else:
if len(self.stateName) > 0:
self.onechar = self.stateName[0]
else:
self.onechar = "?"
self.startProbability = self.mathType(dictionary["startprob"])
self.endProbability = self.mathType(dictionary["endprob"])
self.emissions = dict()
for [key, prob] in dictionary["emission"]:
if key.__class__.__name__ == "list":
key = tuple(key)
try:
self.emissions[key] = self.mathType(prob)
except ValueError:
self.emissions[key] = prob
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "sequences" not in dictionary:
raise ParseException("Sequences not in AnnotationConfig")
self.annotations = dictionary['annotations']
self.sequences = dict()
for i in dictionary["sequences"]:
self.sequences[i['name']] = dict()
for a in i['annotations']:
if a['id'] in self.annotations:
if 'offset' in a:
offset = a['offset']
else:
offset = 0
self.sequences[i['name']][a['id']] = (a['file'], offset)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "sequences" not in dictionary:
raise ParseException("Sequences not in AnnotationConfig")
self.annotations = dictionary['annotations']
self.sequences = dict()
for i in dictionary["sequences"]:
self.sequences[i['name']] = dict()
for a in i['annotations']:
if a['id'] in self.annotations:
if 'offset' in a:
offset = a['offset']
else:
offset = 0
self.sequences[i['name']][a['id']] = (a['file'], offset)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
#Detect if user provides the data or not
start = 0
if 'start' in dictionary:
start = float(dictionary['start'])
if 'data' not in dictionary:
if 'p' not in dictionary:
raise ParseException(
'Probability is missing in RepeatLengthDistribution')
p = float(dictionary['p'])
if 'fractions' not in dictionary:
raise ParseException(
'Fractions are missing in RepeatLengthDistribution')
fractions = dictionary['fractions']
self.setParams(p, start, fractions)
else:
data = dictionary['data']
if 'fractionssize' not in dictionary:
raise ParseException(
'Number of fractions is missing in RepeatLengthDistribution'
)
self.train(data, int(dictionary['fractionssize']), start)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if 'val' not in dictionary:
raise ParseException("Value ('val') not found in state")
self.value = float(dictionary['val'])
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if 'val' not in dictionary:
raise ParseException("Value ('val') not found in state")
self.value = float(dictionary['val'])
def load(self, dictionary):
ConfigObject.load(self, dictionary)
self.loadStates(dictionary)
self.loadTransitions(dictionary)
