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) #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) self.loadStates(dictionary) self.loadTransitions(dictionary)