Source code for Transcript

import configuration as conf

from pyGenoObjectBases import *

import rabaDB.fields as rf

from tools import UsefulFunctions as uf
from Exon import *
from SNP import SNP_INDEL

from tools.BinarySequence import NucBinarySequence


[docs]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
[docs]class Transcript(pyGenoRabaObjectWrapper) : """The wrapper for playing with Transcripts""" _wrapped_class = Transcript_Raba def __init__(self, *args, **kwargs) : pyGenoRabaObjectWrapper.__init__(self, *args, **kwargs) self.exons = RLWrapper(self, Exon, self.wrapped_object.exons) self._load_sequencesTriggers = set(["UTR5", "UTR3", "cDNA", "sequence"]) self.exonsDict = {} def _makeLoadQuery(self, objectType, *args, **coolArgs) : if issubclass(objectType, SNP_INDEL) : # conf.db.enableDebug(True) 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 _load_sequences(self) : def getV(k) : return pyGenoRabaObjectWrapper.__getattribute__(self, k) def setV(k, v) : return pyGenoRabaObjectWrapper.__setattr__(self, k, v) sequence = [] cDNA = [] UTR5 = [] UTR3 = [] exons = [] prime5 = True for ee in self.wrapped_object.exons : e = pyGenoRabaObjectWrapper_metaclass._wrappers[Exon_Raba](wrapped_object_and_bag = (ee, getV('bagKey'))) self.exonsDict[(e.start, e.end)] = e exons.append(e) sequence.append(e.sequence) if e.hasCDS() : UTR5.append(e.UTR5) cDNA.append(e.CDS) UTR3.append(e.UTR3) prime5 = False else : if prime5 : UTR5.append(e.sequence) else : UTR3.append(e.sequence) sequence = ''.join(sequence) cDNA = ''.join(cDNA) UTR5 = ''.join(UTR5) UTR3 = ''.join(UTR3) setV('exons', exons) setV('sequence', sequence) setV('cDNA', cDNA) setV('UTR5', UTR5) setV('UTR3', UTR3) if len(cDNA) > 0 and len(cDNA) % 3 != 0 : setV('flags', {'DUBIOUS' : True, 'cDNA_LEN_NOT_MULT_3': True}) else : setV('flags', {'DUBIOUS' : False, 'cDNA_LEN_NOT_MULT_3': False}) def _load_bin_sequence(self) : self.bin_sequence = NucBinarySequence(self.sequence) self.bin_UTR5 = NucBinarySequence(self.UTR5) self.bin_cDNA = NucBinarySequence(self.cDNA) self.bin_UTR3 = NucBinarySequence(self.UTR3)
[docs] def getNucleotideCodon(self, cdnaX1) : """Returns the entire codon of the nucleotide at pos cdnaX1 in the cdna, and the position of that nocleotide in the codon""" return uf.getNucleotideCodon(self.cDNA, cdnaX1)
[docs] def getCodon(self, i) : """returns the ith codon""" return self.getNucleotideCodon(i*3)[0]
[docs] def iterCodons(self) : """iterates through the codons""" for i in range(len(self.cDNA)/3) : yield self.getCodon(i)
[docs] def find(self, sequence) : """return the position of the first occurance of sequence""" return self.bin_sequence.find(sequence)
[docs] def findAll(self, sequence): """Returns a list of all positions where sequence was found""" return self.bin_sequence.findAll(sequence)
[docs] def findIncDNA(self, sequence) : """return the position of the first occurance of sequence""" return self.bin_cDNA.find(sequence)
[docs] def findAllIncDNA(self, sequence) : """Returns a list of all positions where sequence was found in the cDNA""" return self.bin_cDNA.findAll(sequence)
[docs] def getcDNALength(self) : """returns the length of the cDNA""" return len(self.cDNA)
[docs] def findInUTR5(self, sequence) : """return the position of the first occurance of sequence in the 5'UTR""" return self.bin_UTR5.find(sequence)
[docs] def findAllInUTR5(self, sequence) : """Returns a list of all positions where sequence was found in the 5'UTR""" return self.bin_UTR5.findAll(sequence)
[docs] def getUTR5Length(self) : """returns the length of the 5'UTR""" return len(self.bin_UTR5)
[docs] def findInUTR3(self, sequence) : """return the position of the first occurance of sequence in the 3'UTR""" return self.bin_UTR3.find(sequence)
[docs] def findAllInUTR3(self, sequence) : """Returns a lits of all positions where sequence was found in the 3'UTR""" return self.bin_UTR3.findAll(sequence)
[docs] def getUTR3Length(self) : """returns the length of the 3'UTR""" return len(self.bin_UTR3)
[docs] def getNbCodons(self) : """returns the number of codons in the transcript""" return len(self.cDNA)/3
def __getattribute__(self, name) : return pyGenoRabaObjectWrapper.__getattribute__(self, name) def __getitem__(self, i) : return self.sequence[i] def __len__(self) : return len(self.sequence) def __str__(self) : return """Transcript, id: %s, name: %s > %s""" %(self.id, self.name, str(self.gene))