def test_spoof_maxent_motifs():
trials = 1000
motif = [
'CGGTGAACTA', 'CGGTGTGCGA', 'CGCTGTGCTG', 'CGGGATGCAA', 'CACGCTACGA',
'CGCTATGCTA', 'CGGTTGGCTA', 'CGGCGTGCTA', 'CGGTATATTG', 'CGGGTTGCGA'
]
given_ic = motif_ic(motif) # ~ 9.05 bits
motifs = spoof_maxent_motifs(motif, trials)
lb, ub = mean_ci(map(motif_ic, motifs))
assert lb < given_ic < ub
def test_spoof_motif_cftp():
motif = [
'CGGTGAACTA', 'CGGTGTGCGA', 'CGCTGTGCTG', 'CGGGATGCAA', 'CACGCTACGA',
'CGCTATGCTA', 'CGGTTGGCTA', 'CGGCGTGCTA', 'CGGTATATTG', 'CGGGTTGCGA'
]
given_ic = motif_ic(motif) # ~ 9.05 bits
motifs = spoof_motif_cftp(motif, num_motifs=1000)
spoof_ics = map(motif_ic, motifs)
lb, ub = mean_ci(spoof_ics)
print lb, given_ic, ub
assert_less_equal(lb - 1, given_ic)
assert_less_equal(given_ic, ub + 1)
def test_spoof_motif_cftp_occ():
motif = [
'CGGTGAACTA', 'CGGTGTGCGA', 'CGCTGTGCTG', 'CGGGATGCAA', 'CACGCTACGA',
'CGCTATGCTA', 'CGGTTGGCTA', 'CGGCGTGCTA', 'CGGTATATTG', 'CGGGTTGCGA'
]
bio_matrix = matrix_from_motif(motif)
N = len(motif)
print occupancies
mean_bio_occ = mean(occupancies(motif))
motifs = spoof_motif_cftp_occ(motif, num_motifs=100)
spoof_occs = map(lambda m: mean(occupancies(m)), motifs)
lb, ub = mean_ci(spoof_occs)
print lb, mean_bio_occ, ub
assert_less_equal(lb, mean_bio_occ)
assert_less_equal(mean_bio_occ, ub)
def test_spoof_maxent_motifs():
trials = 1000
motif = ['CGGTGAACTA',
'CGGTGTGCGA',
'CGCTGTGCTG',
'CGGGATGCAA',
'CACGCTACGA',
'CGCTATGCTA',
'CGGTTGGCTA',
'CGGCGTGCTA',
'CGGTATATTG',
'CGGGTTGCGA']
given_ic = motif_ic(motif) # ~ 9.05 bits
motifs = spoof_maxent_motifs(motif,trials)
lb, ub = mean_ci(map(motif_ic,motifs))
assert lb < given_ic < ub
def test_spoof_motif_cftp():
motif = ['CGGTGAACTA',
'CGGTGTGCGA',
'CGCTGTGCTG',
'CGGGATGCAA',
'CACGCTACGA',
'CGCTATGCTA',
'CGGTTGGCTA',
'CGGCGTGCTA',
'CGGTATATTG',
'CGGGTTGCGA']
given_ic = motif_ic(motif) # ~ 9.05 bits
motifs = spoof_motif_cftp(motif, num_motifs=1000)
spoof_ics = map(motif_ic, motifs)
lb, ub = mean_ci(spoof_ics)
print lb, given_ic, ub
assert_less_equal(lb - 1, given_ic)
assert_less_equal(given_ic, ub + 1)
def test_spoof_motif_cftp_occ():
motif = ['CGGTGAACTA',
'CGGTGTGCGA',
'CGCTGTGCTG',
'CGGGATGCAA',
'CACGCTACGA',
'CGCTATGCTA',
'CGGTTGGCTA',
'CGGCGTGCTA',
'CGGTATATTG',
'CGGGTTGCGA']
bio_matrix = matrix_from_motif(motif)
N = len(motif)
print occupancies
mean_bio_occ = mean(occupancies(motif))
motifs = spoof_motif_cftp_occ(motif, num_motifs=100)
spoof_occs = map(lambda m:mean(occupancies(m)), motifs)
lb, ub = mean_ci(spoof_occs)
print lb, mean_bio_occ, ub
assert_less_equal(lb, mean_bio_occ)
assert_less_equal(mean_bio_occ, ub)
def test_maxent_motif():
trials = 1000
N, L, desired_ic = 10, 10, 10
motifs = [maxent_motif(N, L, desired_ic) for i in trange(trials)]
lb, ub = mean_ci(map(motif_ic, motifs))
assert lb < desired_ic < ub
def test_maxent_motif():
trials = 1000
N, L, desired_ic = 10,10,10
motifs = [maxent_motif(N,L,desired_ic) for i in trange(trials)]
lb, ub = mean_ci(map(motif_ic,motifs))
assert lb < desired_ic < ub