def print_meme_motif(word, nsites, ev_string, aln, alph):
# make the PWM
pwm = sequence.PWM(alph)
pwm.setFromAlignment(aln)
# print PWM in MEME format
alen = alph.getLen()
w = len(word)
print("\nMOTIF %s\nletter-probability matrix: alength= %d w= %d nsites= %d E= %s" % \
(word, alen, w, nsites, ev_string))
for row in pwm.pretty():
print(row)
print("")
def get_freqs_and_nsites(w, dists, offsets, seqs, alph):
"""
Get PWMs and numbers of sites for each exact Hamming distance.
Returns (freqs[d], nsites[d]).
"""
freqs = []
nsites = []
# iterate over hamming distances
for d in range(w+1):
# get alignments for a hamming distance == d
aln = get_aln_from_dists_and_offsets(w, d, d, dists, offsets, seqs, alph)
# make frequency matrix
pwm = sequence.PWM(alph)
pwm.setFromAlignment(aln)
freqs.append(pwm.getFreq())
nsites.append(len(aln))
#print "getting freqs for d", d
return freqs, nsites
