We want to compute partitions on a set of sequences from a HMM, and
compute proportions from the resulting partitions.
-
We load the sequences and the HMM.
import lsequence
ls=lsequence.Lsequence()
ls.read_nf('seq_hmm.fa')
import lcompte
lpr=lcompte.Lproportion(fic="lprop2")
print lpr
We notice that in these proportions there is no transition
proportion for the sequences beginning.
- We compute a Lpartition with Viterbi algorithm, and print the
number of segments of each partition
import lpartition
lpa=lpartition.Lpartition()
lpa.add_Lseq(ls)
import lexique
lx=lexique.Lexique()
lx.read_Lprop(lpr)
lpa.viterbi(lx)
for i in lpa:
print len(i[1]),
- We build a new Lcompte of 2-length words from the segmentations.
lc=lcompte.Lcompte()
lc.read_Lpart(lpa,2)
print lc
- We compute a new HMM from the 1|1-proportions on the latter
Lcompte.
lpr2=lcompte.Lproportion()
lpr2.read_Lcompte(lc.rstrip(),lprior=1,lpost=1)
- We compute the Kullback-Leibler divergence form lpr to
lpr2, using MC simulation on 100 sequences of length 5000.
lpr.KL_MC(lpr2,100,5000)
- On the studied sequences, we compute new partitions with this
new HMM with FB algorithm.
lx2=lexique.Lexique()
lx2.read_Lprop(lpr2)
lpa2=lpartition.Lpartition()
lpa2.add_Lseq(lpa.Lseq())
lpa2.fb(lx2)
- And so on.
