Source code for Gene

import configuration as conf

from pyGenoObjectBases import *
from SNP import SNP_INDEL

import rabaDB.fields as rf

[docs]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()
[docs]class Gene(pyGenoRabaObjectWrapper) : """The wrapper for playing with genes""" _wrapped_class = Gene_Raba def __init__(self, *args, **kwargs) : pyGenoRabaObjectWrapper.__init__(self, *args, **kwargs) def _makeLoadQuery(self, objectType, *args, **coolArgs) : if issubclass(objectType, SNP_INDEL) : f = RabaQuery(objectType, namespace = self._wrapped_class._raba_namespace) coolArgs['species'] = self.genome.species coolArgs['chromosomeNumber'] = self.chromosome.number coolArgs['start >='] = self.start coolArgs['start <'] = self.end if len(args) > 0 and type(args[0]) is types.ListType : for a in args[0] : if type(a) is types.DictType : f.addFilter(**a) else : f.addFilter(*args, **coolArgs) return f return pyGenoRabaObjectWrapper._makeLoadQuery(self, objectType, *args, **coolArgs) def __str__(self) : return "Gene, name: %s, id: %s, strand: '%s' > %s" %(self.name, self.id, self.strand, str(self.chromosome))