def write_weblogo(self, filepath):
matrix_tuple = []
for distribution in self.values:
matrix_tuple.append(tuple(distribution))
dataArray = np.array(tuple(matrix_tuple))
alph = Alphabet(''.join(self.alphabet))
weblogoData = LogoData.from_counts(alph, dataArray)
weblogoOptions = LogoOptions(color_scheme=classic)
weblogoOptions.title = "PWM"
weblogoFormat = LogoFormat(weblogoData, weblogoOptions)
weblogo_file = open(filepath, 'w')
weblogo_file.write(png_print_formatter(weblogoData, weblogoFormat))
weblogo_file.close()
def outputMotif(theta_motif, theta_background_matrix, lambda_motif, logev, k, outstr):
from weblogolib import LogoData, LogoOptions, LogoFormat, png_formatter, eps_formatter, unambiguous_dna_alphabet
_pv_format = "%3.1fe%+04.0f"
f_string = sprint_logx(log(lambda_motif), 1, _pv_format)
g_string = sprint_logx(logev, 1, _pv_format)
print(("Motif {0:s} had a fraction of {1:s}").format(str(k), f_string))
print(("Motif {0:s} had an E-value of {1:s}").format(str(k), g_string))
print 'Saving motif as a png...'
data = LogoData.from_counts(counts=theta_motif,alphabet=unambiguous_dna_alphabet)#,prior=theta_background_matrix[0])#Does prior mess things up?
options = LogoOptions()
options.title = 'Motif'
forma = LogoFormat(data, options)
fout = open(outstr + "Motif_" + str(k) + '.png', 'w')
png_formatter(data, forma, fout)
fout.close()
print 'Saving motif as an eps...'
fout = open(outstr + "Motif_" + str(k) + '.eps', 'w')
eps_formatter(data, forma, fout)
fout.close()
def outputMotif(theta_motif, theta_background_matrix, lambda_motif, logev, k, outstr):
from weblogolib import LogoData, LogoOptions, LogoFormat, png_formatter, eps_formatter, unambiguous_dna_alphabet
_pv_format = "%3.1fe%+04.0f"
f_string = sprint_logx(log(lambda_motif), 1, _pv_format)
g_string = sprint_logx(logev, 1, _pv_format)
print(("Motif {0:s} had a fraction of {1:s}").format(str(k), f_string))
print(("Motif {0:s} had an E-value of {1:s}").format(str(k), g_string))
print 'Saving motif as a png...'
data = LogoData.from_counts(counts=theta_motif,alphabet=unambiguous_dna_alphabet)#,prior=theta_background_matrix[0])#Does prior mess things up?
options = LogoOptions()
options.title = 'Motif'
forma = LogoFormat(data, options)
fout = open(outstr + "Motif_" + str(k) + '.png', 'w')
png_formatter(data, forma, fout)
fout.close()
print 'Saving motif as an eps...'
fout = open(outstr + "Motif_" + str(k) + '.eps', 'w')
eps_formatter(data, forma, fout)
fout.close()
