Esempio n. 1
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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;
Esempio n. 2
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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
Esempio n. 3
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def GetKmerFromMotifFromPWM(pwm, seq):
	m = MotifTools.toDict(pwm)
	#print m
	motif = MotifTools.Motif_from_counts(m)
	return motif.bestscanseq(seq);