def test_slice_to_ref():
test_base = 'ACTGTTgggTTGCGTA'
test_ref = 'ACTGTTTTGCGTA'
start = 4
stop = 8
res = TFSeqTools.slice_to_ref(test_ref, start, stop, test_ref)
yield eq_, test_ref[4:8].lower(), res.lower(), 'Simple Slice is wrong!'
expect = 'TTgggTT'
res = TFSeqTools.slice_to_ref(test_ref, start, stop, test_base)
yield eq_, expect.lower(), res.lower(), 'Aligned Slice is wrong!'
def region_extractor(conb_ltr, start, stop, seq):
oseq = TFSeqTools.slice_to_ref(seq, conb_ltr, start, stop)
nseq = oseq.replace('-', '')
if len(nseq):
return nseq
else:
return np.nan
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 test_align_to_ref():
test_base = 'ACTGTTTTGCGTA'
test_ref = 'ACTGTTgTTGCGTA'
res_base = 'ACTGTT-TTGCGTA'
res_ref = 'ACTGTTgTTGCGTA'
out_base, out_ref = TFSeqTools.align_to_ref(test_ref, test_base)
tests = [(eq_, res_base.lower(), out_base.lower(),
'Query alignment was wrong!'),
(eq_, res_ref.lower(), out_ref.lower(),
'Reference alignment was wrong!'),
(ok_, (test_ref, test_base) in TFSeqTools.align_to_ref,
'Memoization didnt save properly'),
(eq_, TFSeqTools.align_to_ref[(test_ref, test_base)],
(out_base, out_ref), 'Memoization saved wrong data!')
]
for tup in tests:
yield tup
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'])
def check_rev_mot(key, mot):
rmot = TFSeqTools.true_motif_rev_complement(mot)
rscore = rmot.pssm.calculate(rmot.consensus)
fscore = mot.pssm.calculate(mot.consensus)
eq_(rscore, fscore, '%s was not reversed properly!' % key)