Exemple #1
0
 def getTFBSbyRatio(self, sequence, minscore_percent=0.1):
     """returns the hits, which are better then log2(minscore_percent*maxprod)
     
     These are possible Transcription Factor Binding Sites. The formula is equal
     to log2(minscore_percent)+maxscore"""
     minscore=log2(minscore_percent)
     #self.setBG(sequence)
     print "Max Score: %f Cutoff: %f"%(self.maxscore,minscore+self.maxscore)
     #seqIO=StringIO(sequence)
     #seqIO.seek(0)
     #seqIO=open("/home/kpalin/tyot/comparative/mabs/iso.tmp.fa")
     #seqIO.seek(1)
     ret=_c_matrix.getTFBSwithBg(self.M_weight, sequence, minscore+self.maxscore,Matrix.backGround)
     if not ret:
         ret={}
     if ret.has_key("NEXT_SEQ"):
         print "NEXT_SEQ",ret["NEXT_SEQ"]
         del ret["NEXT_SEQ"]
     return ret
Exemple #2
0
    def getTFBSbyAbsolute(self,sequence,cutoff):
        """Returns the hits that are better than cutoff"""
        #self.setBG(sequence)
        #self.initWeights()
        print "Max Score: %f Cutoff: %f"%(self.maxscore,cutoff)
        #seqIO=StringIO(sequence)
        #seqIO.seek(0)
        
        #self.initWeights(0)

        
        if self.maxscore>cutoff:
            #bg=matrix.BackGround(open("/home/kpalin/tyot/comparative/humanGenome/chr1.fa"))
            ret=_c_matrix.getTFBSwithBg(self.M_weight,sequence,cutoff,Matrix.backGround)
            #ret=matrix.getTFBS(self.M_weight,sequence,cutoff)
            if ret.has_key("NEXT_SEQ"):
                print "NEXT_SEQ",ret["NEXT_SEQ"]
                del ret["NEXT_SEQ"]
        else:
            ret={}
        return ret