Esempio n. 1
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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!'
Esempio n. 2
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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
Esempio n. 3
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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!'
Esempio n. 4
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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
Esempio n. 5
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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'])
Esempio n. 6
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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)