def setFrequencies(model, mali, prefix=""):
"""set frequencies in a model according to those observed in data.
prefix: prefix for rate parameters.
Frequencies are labelled:
pa0, pc0, ..., pa1, pc1, ..., pa2, pc2, ...
"""
try:
frequencies = Codons.getFrequenciesPerCodonPosition(
[x.mString for x in mali.values()])
except XGram.Exceptions.UsageError:
return
## build a dummy grammar to insert frequencies
dummy_grammar = XGram.Model.Grammar()
for x in range(0, 3):
params = []
for a in ('A', 'C', 'G', 'T'):
params.append(
("%sp%s%i" % (prefix, a.lower(), x), frequencies[x][a]))
dummy_grammar.addVariable(params)
model.mGrammar.copyParameters(dummy_grammar, ignore_missing=True)
def setFrequencies(model, mali, prefix=""):
"""set frequencies in a model according to those observed in data.
prefix: prefix for rate parameters.
Frequencies are labelled:
pa0, pc0, ..., pa1, pc1, ..., pa2, pc2, ...
"""
try:
frequencies = Codons.getFrequenciesPerCodonPosition(
[x.mString for x in list(mali.values())])
except XGram.Exceptions.UsageError:
return
# build a dummy grammar to insert frequencies
dummy_grammar = XGram.Model.Grammar()
for x in range(0, 3):
params = []
for a in ('A', 'C', 'G', 'T'):
params.append(
("%sp%s%i" % (prefix, a.lower(), x), frequencies[x][a]))
dummy_grammar.addVariable(params)
model.mGrammar.copyParameters(dummy_grammar,
ignore_missing=True)
def setFrequencies( model, data):
"""set frequencies in a model according to those observed in data.
"""
sequences = getSequencesFromStk( data )
frequencies = Codons.getFrequenciesPerCodonPosition( sequences.values() )
## build a dummy grammar to insert frequencies
dummy_grammar = XGram.Model.Grammar()
for x in range(0,3):
params = []
for a in ('A', 'C', 'G', 'T'):
params.append( ("P%i%s" % (x, a), frequencies[x][a]) )
dummy_grammar.addVariable( params )
model.mGrammar.copyParameters( dummy_grammar,
ignore_missing = True)
explicit_extension=True,
fix_kappa=options.kappa == None,
fix_omega=options.omega == None)
## set codon usage frequencies
if options.insert_frequencies:
mali = Mali.Mali()
mali.readFromFile(open(options.insert_frequencies, "r"),
format=options.input_format)
if mali.getLength() == 0:
raise "refusing to process empty alignment."
frequencies = Codons.getFrequenciesPerCodonPosition(
map(lambda x: x.mString, mali.values()))
# build a dummy grammar to insert frequencies
dummy_grammar = XGram.Model.Grammar()
for x in range(0, 3):
params = []
for a in ('A', 'C', 'G', 'T'):
params.append(
("p%s%i" % (a.lower(), x), frequencies[x][a]))
dummy_grammar.addVariable(params)
input_model.mGrammar.copyParameters(dummy_grammar,
ignore_missing=True)
## count the number of synonymous and non-synonymous sites
if options.omega or options.kappa:
fix_kappa = options.kappa == None,
fix_omega = options.omega == None )
## set codon usage frequencies
if options.insert_frequencies:
mali = Mali.Mali()
mali.readFromFile( open(options.insert_frequencies, "r"),
format = options.input_format )
if mali.getLength() == 0:
raise "refusing to process empty alignment."
frequencies = Codons.getFrequenciesPerCodonPosition( map( lambda x: x.mString, mali.values() ))
# build a dummy grammar to insert frequencies
dummy_grammar = XGram.Model.Grammar()
for x in range(0,3):
params = []
for a in ('A', 'C', 'G', 'T'):
params.append( ("p%s%i" % (a.lower(), x), frequencies[x][a]) )
dummy_grammar.addVariable( params )
input_model.mGrammar.copyParameters( dummy_grammar,
ignore_missing = True)
## count the number of synonymous and non-synonymous sites
if options.omega or options.kappa:
n, s = countSites( input_model )
