def get_response_content(fs):
# deserialize the xml data to create a DirectProteinMixture
try:
mixture_model = DirectProtein.deserialize_mixture_model(fs.model)
except ValueError as e:
raise HandlingError(e)
# Normalize the mixture model to have an expected rate of one
# substitution per unit of branch length.
mixture_model.normalize()
# begin writing the html file
out = StringIO()
# write the html header
print >> out, '<html>'
print >> out, '<head>'
print >> out, '<style type="text/css">td{font-size:x-small;}</style>'
print >> out, '</head>'
print >> out, '<body>'
# write the symmetric components of the rate matrices
for category_i, matrix_object in enumerate(mixture_model.rate_matrices):
codon_v = matrix_object.get_stationary_distribution()
matrix = matrix_object.dictionary_rate_matrix
symmetric_matrix = {}
for ca, pa in zip(codons, codon_v):
for cb, pb in zip(codons, codon_v):
value = matrix[(ca, cb)] / (math.sqrt(pb) / math.sqrt(pa))
symmetric_matrix[(ca, cb)] = value
print >> out, 'the symmetric component of the rate matrix'
print >> out, 'for category %d:' % (category_i + 1)
print >> out, '<table>'
print >> out, RateMatrix.codon_rate_matrix_to_html_string(
symmetric_matrix)
print >> out, '</table>'
print >> out, '<br/><br/>'
# write the html footer
print >> out, '</body>'
print >> out, '</html>'
# return the response
return out.getvalue()
def get_response_content(fs):
# deserialize the xml data to create a DirectProteinMixture
try:
mixture_model = DirectProtein.deserialize_mixture_model(fs.model)
except ValueError as e:
raise HandlingError(e)
# Normalize the mixture model to have an expected rate of one
# substitution per unit of branch length.
mixture_model.normalize()
# begin writing the html file
out = StringIO()
# write the html header
print >> out, '<html>'
print >> out, '<head>'
print >> out, '<style type="text/css">td{font-size:x-small;}</style>'
print >> out, '</head>'
print >> out, '<body>'
# write the symmetric components of the rate matrices
for category_i, matrix_object in enumerate(mixture_model.rate_matrices):
codon_v = matrix_object.get_stationary_distribution()
matrix = matrix_object.dictionary_rate_matrix
symmetric_matrix = {}
for ca, pa in zip(codons, codon_v):
for cb, pb in zip(codons, codon_v):
value = matrix[(ca, cb)] / (math.sqrt(pb) / math.sqrt(pa))
symmetric_matrix[(ca, cb)] = value
print >> out, 'the symmetric component of the rate matrix'
print >> out, 'for category %d:' % (category_i + 1)
print >> out, '<table>'
print >> out, RateMatrix.codon_rate_matrix_to_html_string(
symmetric_matrix)
print >> out, '</table>'
print >> out, '<br/><br/>'
# write the html footer
print >> out, '</body>'
print >> out, '</html>'
# return the response
return out.getvalue()
