def taMotif2MopatMatrix(taMotif):
"""
Uses ONE tamo motif to produce a probability matrix compatible with MOPAT.
RETURNS: [oneLetterName, [list of lists]]
"""
name = taMotif.oneletter.replace('.','n')
matrix = []
# Use logLiklihoods to generate info for motif.counts
taMotif = Motif(taMotif.bogus_kmers())
for pos in taMotif.counts:
mopatPos = []
for nuc in sorted(pos.keys()):
mopatPos.append(pos[nuc])
matrix.append(mopatPos)
return [name, matrix]
from TAMO.MotifTools import Motif
import motility
tM = Motif('WGATAR')
sites = tM.bogus_kmers()
tM = Motif(sites)
mM = motility.make_pwm(sites)
s = 'ATGCATGCTAGCGGCTGATAACGCTTATCATATGC'
mReults = mM.find(s,mM.max_score()*0.75,)
