def get_form():
"""
@return: the body of a form
"""
# define the default xml string
default_xml_string = DirectRna.get_sample_xml_string()
# define the form objects
return [Form.MultiLine('model', 'mixture model', default_xml_string)]
def get_form():
"""
@return: the body of a form
"""
# define the default xml string
default_xml_string = DirectRna.get_sample_xml_string()
# define the form objects
return [Form.MultiLine('model', 'mixture model', default_xml_string)]
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_form():
"""
@return: the body of a form
"""
# define the tree
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip()),
Form.Integer('ncols', 'sample this many columns',
100, low=1, high=10000)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
g_sample_alignment_string.strip()),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip())]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
g_sample_alignment_string.strip()),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip())
]
return form_objects
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'
def get_form():
"""
@return: the body of a form
"""
# define the tree
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip()),
Form.Integer('ncols',
'sample this many columns',
100,
low=1,
high=10000)
]
return form_objects