def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
# get the nucleotide alignment
try:
alignment = Fasta.Alignment(fs.alignment.splitlines())
alignment.force_nucleotide()
except Fasta.AlignmentError as e:
raise HandlingError(e)
# get the normalized Direct RNA mixture model
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
mixture_model.normalize()
# return the html string
return do_analysis(mixture_model, alignment, tree) + '\n'
def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
# get the nucleotide alignment
try:
alignment = Fasta.Alignment(fs.alignment.splitlines())
alignment.force_nucleotide()
except Fasta.AlignmentError as e:
raise HandlingError(e)
# get the normalized Direct RNA mixture model
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
mixture_model.normalize()
# return the html string
return do_analysis(mixture_model, alignment, tree) + '\n'
def get_response_content(fs):
# deserialize the xml data to create a DirectRnaMixture
try:
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
except ValueError as e:
raise HandlingError(e)
expected_rate = mixture_model.get_expected_rate()
nt_distribution = mixture_model.get_nt_stationary_distribution()
# write the summary
out = StringIO()
print >> out, 'expected substitution rate:'
print >> out, expected_rate
print >> out, ''
print >> out, 'nucleotide distribution:'
for nt, proportion in zip(Codon.g_nt_letters, nt_distribution):
print >> out, '%s : %s' % (nt, proportion)
# return the summary
return out.getvalue()
def get_response_content(fs):
# deserialize the xml data to create a DirectRnaMixture
try:
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
except ValueError as e:
raise HandlingError(e)
expected_rate = mixture_model.get_expected_rate()
nt_distribution = mixture_model.get_nt_stationary_distribution()
# write the summary
out = StringIO()
print >> out, 'expected substitution rate:'
print >> out, expected_rate
print >> out, ''
print >> out, 'nucleotide distribution:'
for nt, proportion in zip(Codon.g_nt_letters, nt_distribution):
print >> out, '%s : %s' % (nt, proportion)
# return the summary
return out.getvalue()
def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
# get the normalized Direct RNA mixture model
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
mixture_model.normalize()
# simulate the alignment
try:
alignment = PhyLikelihood.simulate_alignment(tree, mixture_model,
fs.ncols)
except PhyLikelihood.SimulationError as e:
raise HandlingError(e)
# get the alignment
arr = []
for node in tree.gen_tips():
arr.append(alignment.get_fasta_sequence(node.name))
# return the alignment string
return '\n'.join(arr) + '\n'
def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
# get the normalized Direct RNA mixture model
mixture_model = DirectRna.deserialize_mixture_model(fs.model)
mixture_model.normalize()
# simulate the alignment
try:
alignment = PhyLikelihood.simulate_alignment(tree,
mixture_model, fs.ncols)
except PhyLikelihood.SimulationError as e:
raise HandlingError(e)
# get the alignment
arr = []
for node in tree.gen_tips():
arr.append(alignment.get_fasta_sequence(node.name))
# return the alignment string
return '\n'.join(arr) + '\n'
