class Transcript_Raba(pyGenoRabaObject): """The wrapped Raba object that really holds the data""" _raba_namespace = conf.pyGeno_RABA_NAMESPACE id = rf.Primitive() name = rf.Primitive() length = rf.Primitive() start = rf.Primitive() end = rf.Primitive() coding = rf.Primitive() genome = rf.RabaObject('Genome_Raba') chromosome = rf.RabaObject('Chromosome_Raba') gene = rf.RabaObject('Gene_Raba') protein = rf.RabaObject('Protein_Raba') exons = rf.Relation('Exon_Raba') def _curate(self): if self.name != None: self.name = self.name.upper() self.length = abs(self.end - self.start) if self.exons[0].CDS_start is not None and self.exons[ -1].CDS_end is not None: self.coding = True else: self.coding = False
class Protein_Raba(pyGenoRabaObject) : """The wrapped Raba object that really holds the data""" _raba_namespace = conf.pyGeno_RABA_NAMESPACE id = rf.Primitive() name = rf.Primitive() genome = rf.RabaObject('Genome_Raba') chromosome = rf.RabaObject('Chromosome_Raba') gene = rf.RabaObject('Gene_Raba') transcript = rf.RabaObject('Transcript_Raba') def _curate(self) : if self.name != None : self.name = self.name.upper()
class Gene_Raba(pyGenoRabaObject) : _raba_namespace = conf.pyGeno_RABA_NAMESPACE id = rf.Primitive() name = rf.Primitive() strand = rf.Primitive() biotype = rf.Primitive() start = rf.Primitive() end = rf.Primitive() genome = rf.RabaObject('Genome_Raba') chromosome = rf.RabaObject('Chromosome_Raba') def _curate(self) : self.name = self.name.upper()
class Gene_Raba(pyGenoRabaObject): """The wrapped Raba object that really holds the data""" _raba_namespace = conf.pyGeno_RABA_NAMESPACE id = rf.Primitive() name = rf.Primitive() strand = rf.Primitive() biotype = rf.Primitive() start = rf.Primitive() end = rf.Primitive() genome = rf.RabaObject('Genome_Raba') chromosome = rf.RabaObject('Chromosome_Raba') def _curate(self): self.name = self.name.upper()
class Exon_Raba(pyGenoRabaObject): """The wrapped Raba object that really holds the data""" _raba_namespace = conf.pyGeno_RABA_NAMESPACE id = rf.Primitive() number = rf.Primitive() start = rf.Primitive() end = rf.Primitive() length = rf.Primitive() CDS_length = rf.Primitive() CDS_start = rf.Primitive() CDS_end = rf.Primitive() frame = rf.Primitive() strand = rf.Primitive() genome = rf.RabaObject('Genome_Raba') chromosome = rf.RabaObject('Chromosome_Raba') gene = rf.RabaObject('Gene_Raba') transcript = rf.RabaObject('Transcript_Raba') protein = rf.RabaObject('Protein_Raba') def _curate(self): if self.start != None and self.end != None: if self.start > self.end: self.start, self.end = self.end, self.start self.length = self.end - self.start if self.CDS_start != None and self.CDS_end != None: if self.CDS_start > self.CDS_end: self.CDS_start, self.CDS_end = self.CDS_end, self.CDS_start self.CDS_length = self.CDS_end - self.CDS_start if self.number != None: self.number = int(self.number) if not self.frame or self.frame == '.': self.frame = None else: self.frame = int(self.frame)
class Chromosome_Raba(pyGenoRabaObject): _raba_namespace = conf.pyGeno_RABA_NAMESPACE header = rf.Primitive() number = rf.Primitive() start = rf.Primitive() end = rf.Primitive() length = rf.Primitive() genome = rf.RabaObject('Genome_Raba') def _curate(self): if self.end != None and self.start != None: self.length = self.end - self.start if self.number != None: self.number = str(self.number).upper()