def to_gnomic(self):
accession = Target.to_gnomic(self)
if self._value == 0:
feature = Feature(name=self.id, accession=accession, type=Type(self.__gnomic_feature_type__))
return Del(feature)
elif self.fold_change != 0:
feature = Feature(name=self.id, accession=accession, type=Type(self.__gnomic_feature_type__),
variant="value={}".format(self._value))
return Ins(feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(accession=accession,
type=self.__gnomic_feature_type__)
if self._value == 0:
return Del(feature)
elif abs(self._value) > abs(self._reference_value):
over_expression = Feature(accession=accession,
type=self.__gnomic_feature_type__,
variant="over-expression(%f)" %
self.fold_change)
return Mutation(feature, over_expression)
elif abs(self._value) < abs(self._reference_value):
under_expression = Feature(accession=accession,
type=self.__gnomic_feature_type__,
variant="down-regulation(%f)" %
self.fold_change)
return Mutation(feature, under_expression)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(accession=accession, type='reaction')
return Ins(feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
new_accession = Accession(self.id + self.swap_str)
original_feature = Feature(accession=accession, type='reaction')
new_feature = Feature(accession=new_accession, type='reaction')
return Sub(original_feature, new_feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(name=self.id, accession=accession)
return Del(feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(accession=accession, type=Type('reaction'), name=self.id)
return Ins(feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
pairs = [(metabolite1.id, metabolite2.id) for metabolite1, metabolite2 in zip(*self.swap_pairs)]
feature = Feature(name=self.id, accession=accession, type=Type('reaction'),
variant=";".join(["=".join(pair) for pair in pairs]))
return Mutation(old=None, new=feature)