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
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