def Read_Dreme_PSSM(lines): pwm = [] name = "Dreme Motif"; vals = [] for line in lines.split('\n'): for item in line.split(): vals.append(float(item)) pwm.append(vals) vals = []; #print pwm m = MotifTools.toDict(pwm) motif = MotifTools.Motif_from_counts(m) return motif;
def Make_PWM_Motif(filename, motifBackGround=""): #print "# Reading PWM from: [%s]"%filename name, pwm = Read_PWM(filename) m = MotifTools.toDict(pwm) #print m motif = MotifTools.Motif_from_ll(m); motif.source = name #print "Motif:", motif.source #print "Max Motif Score:", motif.maxscore #print "Motif Summary:", motif.summary() #motif.printlogo(2.3,10) return motif
def GetKmerFromMotifFromPWM(pwm, seq): m = MotifTools.toDict(pwm) #print m motif = MotifTools.Motif_from_counts(m) return motif.bestscanseq(seq);