def test_simple_score_pwm():
pwm_dict = TFSeqTools.Load_PWMS()
mot = pwm_dict['arnt']
#A 4 19 0 0 0 0
#C 16 0 20 0 0 0
#G 0 1 0 20 0 20
#T 0 0 0 0 20 0
tseq = 'AAACACGTGAAAA'
cor_seq = 'CACGTG'
cor_pos = tseq.find(cor_seq)
_, bpos, nseq = TFSeqTools.simple_score_pwm(mot, tseq)
yield eq_, bpos, cor_pos, 'Wrong position found!'
yield eq_, nseq, cor_seq, 'Wrong sequence found!'
def scan_seq(mot, name, seq):
if len(seq) < len(mot):
return pd.Series([np.nan, np.nan], index = [name+'-Score', name+'-Seq'])
score, _, seq = TFSeqTools.simple_score_pwm(seq, mot)
return pd.Series([score, seq], index = [name+'-Score', name+'-Seq'])
