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()