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'])