def plotPssm(pssm, fileName):
dist = numpy.array( pssm.getMatrix(), numpy.float64 )
data = LogoData.from_counts(corebio.seq.unambiguous_rna_alphabet, dist*100)
options = LogoOptions()
options.color_scheme = colorscheme.nucleotide
format = LogoFormat(data, options)
with open(fileName, 'w') as fout:
fout.write(png_formatter(data, format))
def plotPssm(pssm, fileName):
dist = numpy.array( pssm.getMatrix(), numpy.float64 )
data = LogoData.from_counts(corebio.seq.unambiguous_dna_alphabet, dist*100)
options = LogoOptions()
options.color_scheme = colorscheme.nucleotide
format = LogoFormat(data, options)
fout = open(fileName, 'w')
png_formatter(data, format, fout)
fout.close()
def ic(pssm,norm=True):
bgFreq = [0.21, 0.29, 0.29, 0.21]
res=0
pwm=pssm.getMatrix()
for i in range(len(pwm)):
res+=2
for a in [0,1,2,3]:
if pwm[i][a]!=0:
if norm==True:
res+=pwm[i][a]*math.log(pwm[i][a]/bgFreq[a],2)
else:
res+=pwm[i][a]*math.log(pwm[i][a],2)
return res