if __name__ == "__main__":
hmm = HMM()
# Set the params of the h,,
set_params_hmm_exp1(hmm)
cmrf = CMRF(hmm)
seq1 = "a" * 12
feat1 = "HHHHLLLLHHHH"
seq2 = "b" * 12
feat2 = "BBBBLLLLBBBB"
# Plot the entire sequence space
ll_list1, ll_list2 = [], []
for seq in product("ab", repeat=12):
ll_list1.append(cmrf.score(seq, feat1))
ll_list2.append(cmrf.score(seq, feat2))
# Find the pareto frontier
frontier, frontier_energy = pareto_frontier(cmrf, [feat1, feat2])
pl.figure()
pl.plot(ll_list1, ll_list2, "b*")
pl.plot(*zip(*sorted(frontier_energy)), color="magenta", marker="*", linestyle="dashed")
ctr = dict(zip(set(frontier_energy), [0] * len(set(frontier_energy))))
for i, e in enumerate(frontier_energy):
ctr[e] += 1
if i == 0:
pl.text(e[0] + 0.5, e[1] - 0.4, str(i), fontsize=10)
pl.text(e[0] - 3, e[1] + 0.8, frontier[i], fontsize=9)
else:
set_params_hmm_exp1(hmm)
cmrf = CMRF(hmm)
seq1 = 'a' * 12
feat1 = 'HHHHLLLLHHHH'
seq2 = 'b' * 12
feat2 = 'BBBBLLLLBBBB'
### DEBUG
import pickle
cmrf = pickle.load(open('cmrf.pkl'))
# Plot the entire sequence space
ll_list1, ll_list2 = [], []
seq_list = ["".join(s) for s in product('ab', repeat=12)]
for seq in seq_list:
ll_list1.append(cmrf.score(seq, feat1))
ll_list2.append(cmrf.score(seq, feat2))
min_feat1id = ll_list1.index(min(ll_list1))
min_feat2id = ll_list2.index(min(ll_list2))
# Find the pareto frontier
frontier, frontier_energy = pareto_frontier(cmrf, [feat1, feat2])
# Plot only the frontier
pl.figure()
pl.plot(*zip(*sorted(frontier_energy)),color='magenta',marker='*',\
linestyle='dashed')
ctr = dict(zip(set(frontier_energy), [0] * len(set(frontier_energy))))
for i, e in enumerate(frontier_energy):
ctr[e] += 1
hmm.trans[-1][-1].append(val)
return hmm
if __name__ == '__main__':
b = BoostedHMM()
hmm1, hmm2 = b.hmm1, b.hmm2
# Set the params of the hmm
cmrf1 = CMRF(hmm1)
cmrf2 = CMRF(hmm2)
feat = 'HHHHHHHHHHHH'
# Plot the entire sequence space
ll_list1, ll_list2 = [], []
for seq in product('ab', repeat=12):
ll_list1.append(cmrf1.score(seq, feat))
ll_list2.append(cmrf2.score(seq, feat))
ll_list3, ll_list4 = [], []
for seq in b.kseqlist:
ll_list3.append(cmrf1.score(seq, feat))
ll_list4.append(cmrf2.score(seq, feat))
pl.figure()
pl.plot(ll_list1, ll_list2, 'b*')
pl.plot(ll_list3, ll_list4, 'r*')
pl.xlabel('Energy1:')
pl.ylabel('Energy2:')
pl.title('Energy Plot')
xmin, xmax = pl.xlim()
ymin, ymax = pl.ylim()
val = (counts2[i].get(aa1+aa2,0)+self.smoothfac) / (counts[i].get(aa1,0)+self.smoothfac*len(hmm.alphabet))
hmm.trans[-1][-1].append(val)
return hmm
if __name__ == '__main__' :
b = BoostedHMM()
hmm1,hmm2 = b.hmm1,b.hmm2
# Set the params of the hmm
cmrf1 = CMRF(hmm1)
cmrf2 = CMRF(hmm2)
feat = 'HHHHHHHHHHHH'
# Plot the entire sequence space
ll_list1,ll_list2 = [],[]
for seq in product('ab',repeat=12):
ll_list1.append(cmrf1.score(seq,feat))
ll_list2.append(cmrf2.score(seq,feat))
ll_list3,ll_list4 = [],[]
for seq in b.kseqlist:
ll_list3.append(cmrf1.score(seq,feat))
ll_list4.append(cmrf2.score(seq,feat))
pl.figure()
pl.plot(ll_list1,ll_list2,'b*')
pl.plot(ll_list3,ll_list4,'r*')
pl.xlabel('Energy1:')
pl.ylabel('Energy2:')
pl.title('Energy Plot')
xmin,xmax = pl.xlim()
