def print_meme_motif(word, nsites, ev_string, aln):
# make the PWM
pwm = sequence.PWM(sequence.getAlphabet('DNA'))
pwm.setFromAlignment(aln)
# print PWM in MEME format
alphabet = sequence.getAlphabet('DNA').getSymbols()
alen = len(alphabet)
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 print_meme_motif(word, nsites, ev_string, aln):
# make the PWM
pwm = sequence.PWM(sequence.getAlphabet('DNA'))
pwm.setFromAlignment(aln)
# print PWM in MEME format
alphabet = sequence.getAlphabet('DNA').getSymbols()
alen = len(alphabet)
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):
"""
Get PWMs and numbers of sites for each exact Hamming distance.
Returns (freqs[d], nsites[d]).
"""
freqs = []
nsites = []
for d in range(w+1): # Hamming distance
# get alignments
aln = get_aln_from_dists_and_offsets(w, d, d, dists, offsets, seqs)
# make frequency matrix
#FIXME alphabet
pwm = sequence.PWM(sequence.getAlphabet('DNA'))
pwm.setFromAlignment(aln)
freqs.append(pwm.getFreq())
nsites.append(len(aln))
#print "getting freqs for d", d
return freqs, nsites
def get_freqs_and_nsites(w, dists, offsets, seqs):
"""
Get PWMs and numbers of sites for each exact Hamming distance.
Returns (freqs[d], nsites[d]).
"""
freqs = []
nsites = []
for d in range(w + 1): # Hamming distance
# get alignments
aln = get_aln_from_dists_and_offsets(w, d, d, dists, offsets, seqs)
# make frequency matrix
#FIXME alphabet
pwm = sequence.PWM(sequence.getAlphabet('DNA'))
pwm.setFromAlignment(aln)
freqs.append(pwm.getFreq())
nsites.append(len(aln))
#print "getting freqs for d", d
return freqs, nsites
def print_meme_header():
alphabet = "".join(sequence.getAlphabet('DNA').getSymbols())
print >> sys.stdout, "\nMEME version 4.5\n\nALPHABET= %s\n\nstrands: + -\n\nBackground letter frequencies (from" % alphabet
# FIXME: put in real background frequencies
print >> sys.stdout, "A 0.25 C 0.25 G 0.25 T 0.25\n"
def print_meme_header():
alphabet = "".join(sequence.getAlphabet('DNA').getSymbols())
print >> sys.stdout, "\nMEME version 4.5\n\nALPHABET= %s\n\nstrands: + -\n\nBackground letter frequencies (from" % alphabet
# FIXME: put in real background frequencies
print >> sys.stdout, "A 0.25 C 0.25 G 0.25 T 0.25\n"