def run(self):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Simulates a DNA dataset and stores it in NEXUS format in the supplied
filename.
"""
self.starting_tree_source = self.opts.tree_source
self.getStartingTree()
ntax = len(self.opts.taxon_labels)
self.phycassert(ntax > 3, 'Must specify labels for at least four taxa')
ntips = self.starting_tree.getNTips()
if self.starting_tree.isRooted():
ntips -= 1
self.phycassert(ntax == ntips, 'Number of tips in tree (%d) does not match number of taxon labels in taxon_labels (%d)' % (ntips,ntax))
core = LikelihoodCore(self)
core.setupCore()
if not core.tree.hasEdgeLens():
tm = phylogeny.TreeManip(core.tree)
tm.setRandomEdgeLengths(self.opts.edgelen_dist)
self.sim_model_tree = core.tree
core.prepareForSimulation()
sim_data = core.simulate()
sim_data.saveToNexusFile(self.opts.file_name, self.opts.taxon_labels, 'dna', ('a','c','g','t'))
dataf = open(self.opts.file_name,'a')
dataf.write('\n[\ntree used for simulation:\n%s\n]\n' % core.tree.makeNewick() )
dataf.close()
def run(self):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Computes the log-likelihood based on the current tree and current
model.
"""
ds = self.opts.data_source
mat = ds and ds.getMatrix() or None
self.phycassert(self.opts.data_source is not None, "specify data_source before calling like()")
self._loadData(mat)
self.starting_tree = self.getStartingTree()
if self.opts.preorder_edgelens is not None:
self.starting_tree.replaceEdgeLens(self.opts.preorder_edgelens)
print '@@@@@@@@@@ self.starting_tree.makeNewick() =',self.starting_tree.makeNewick()
core = LikelihoodCore(self)
core.setupCore()
core.prepareForLikelihood()
if self.opts.store_site_likes:
core.likelihood.storeSiteLikelihoods(True)
self.opts.pattern_counts = None
self.opts.char_to_pattern = None
self.opts.site_likes = None
self.opts.site_uf = None
else:
core.likelihood.storeSiteLikelihoods(False)
lnL = core.calcLnLikelihood()
if self.opts.store_site_likes:
self.opts.pattern_counts = core.likelihood.getPatternCounts()
self.opts.char_to_pattern = core.likelihood.getCharIndexToPatternIndex()
self.opts.site_likes = core.likelihood.getSiteLikelihoods()
self.opts.site_uf = core.likelihood.getSiteUF()
return lnL
def run(self):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Performs simulations and computes the Gelfand-Ghosh measures Pm, Gm,
and Dm = Pm + Gm for the parameters and trees specified when this
object was created.
"""
self.outputHeader()
# Check to make sure user specified an input tree file
input_trees = self.opts.trees
self.stdout.phycassert(input_trees is not None, 'trees cannot be None when gg is called')
self.stdout.phycassert(input_trees.__class__.__name__ == 'TreeCollection', 'trees must be a TreeCollection object')
# Check to make sure user specified an input params file
input_params = self.opts.params
self.stdout.phycassert(input_params is not None and len(input_params) > 0, 'params cannot be None or empty when gg is called')
# Store transformed edge lengths and parameter values in dictionaries self.edge_lengths and self.parameters, respectively
print 'Harvesting trees and parameters...'
self.harvestTreesAndParams(input_trees, input_params)
# Build list of tuples (t,n) where t is the tree id and n is the frequency of that tree in the sample
tree_id_samplesize_tuples = []
for tid in self.parameters.keys():
tree_id_samplesize_tuples.append((tid,self.sample_size[tid]))
# Sort list so that most commonly-encountered tree topology is first
tree_id_samplesize_tuples.sort(cmp=lambda x,y: cmp(x[1], y[1]))
tree_id_samplesize_tuples.reverse()
self.loadData()
self.gg_mu.resizePatternVect(self.nchar);
self.curr_treeid, self.n = tree_id_samplesize_tuples[0]
if False:
# Create chain manager and (single) chain; no MCMC being done but the chain knows how to
# interact with the model and compute likelihoods and priors
mcmc_manager = MCMCManager(self)
mcmc_manager.createChains()
cc = self.mcmc_manager.getColdChain()
core = cc.likelihood
core = LikelihoodCore(self)
core.setupCore()
# Check to make sure model hasn't changed since creating the param file
param_names_from_model = core.partition_model.getAllParameterNames()
param_names_from_file = self.parameters[tid][0].keys()
exclude_from_comparison = ['Gen','TL','lnL','lnPrior', '1_external_hyper', '1_internal_hyper', '1_edgelen_hyper']
#print '\n*******************\nparam_names_from_model:',param_names_from_model
#print '\n*******************\nparam_names_from_file:',param_names_from_file
self.phycassert(self.loMismo(param_names_from_model, param_names_from_file, exclude_from_comparison), 'Model differs from the model used to generate parameter file (%s)' % self.last_error)
# Let gg_y contain the observed pattern counts
core.likelihood.addDataTo(self.gg_y)
#POLOLD
#if self.gg_bin_patterns:
# self.gg_binned_y = self.gg_y.getBinnedCounts()
if self.gg_bin_patterns and self.opts.out.bincounts is not None:
self._openBinCountsFile()
#######################
###### TREE LOOP ######
#######################
prev_pct_done = 0.0
prev_secs = 0.0
self.gg_total = 0
stopwatch = probdist.StopWatch()
stopwatch.start()
num_distinct_tree_topologies = len(tree_id_samplesize_tuples)
self.output('Performing posterior-predictive simulations (%d distinct topologies):' % num_distinct_tree_topologies)
for tnum,(tid,sample_size) in enumerate(tree_id_samplesize_tuples):
self.n = sample_size
#self.output('\nEvaluating tree = %d (%s)...' % (tnum+1,sample_size == 1 and '1 sample' or '%d samples' % sample_size))
# Replace the tree in likelihood core
core.setTree(self.tree_objects[tid])
self.curr_tree = core.tree
# Build up dictionary of nodes (self.curr_tree_node) in which keys are split representations and values
# are node objects in self.curr_tree. This will be used later to set edge lengths in the tree.
self.fillTreeNodeDict()
# Prepare tree for likelihood calculation by allocating tip and internal data structures
core.likelihood.prepareForLikelihood(self.curr_tree)
#core.likelihood.prepareForSimulation(self.curr_tree)
#########################
###### SAMPLE LOOP ######
#########################
for param_map,edgelen_map in zip(self.parameters[tid],self.edge_lengths[tid]):
# Report progress so user doesn't give up
pct_done = 100.0*float(self.gg_total)/float(self.opts.nreps*self.nsamples)
if pct_done - prev_pct_done >= 10.0:
prev_pct_done = pct_done
secs = stopwatch.elapsedSeconds()
proportion_finished = pct_done/100.0
proportion_remaining = 1.0 - proportion_finished
eta = secs*proportion_remaining/proportion_finished
self.output(' %.0f%% done (%.1fs remaining)...' % (pct_done, eta))
prev_secs = secs
cum_caltbinned_secs = 0.0
self.setupModel(tid, core, param_map, edgelen_map)
#core.likelihood.storeSiteLikelihoods(True)
#core.likelihood.storeAllCLAs(self.curr_tree)
lnL = core.likelihood.calcLnL(self.curr_tree)
#print '-->',lnL,param_map['lnL']
#siteLnLs = core.likelihood.getSiteLikelihoods()
#counts = core.likelihood.getPatternCounts()
#patterns = core.likelihood.listPatterns()
#doof = open('doof_site_likes.txt','w')
#doof.write('Patterns:\n%s\n\n' % patterns)
#for s,c in zip(siteLnLs,counts):
# doof.write('%g\t%g\n' % (s,c))
#doof.close()
#core.likelihood.debugUncompressedDataInfo("all-site-patterns.txt");
for j in range(self.opts.nreps):
self.gg_num_post_pred_reps += 1.0
self.gg_simdata = core.simulate()
# Save the simulated data set if desired
if self.opts.out.postpred.__bool__():
self._openPostPredFile()
self.gg_simdata.saveToNexusFilePython(self.postpredf, self.taxon_labels, 'dna', ('a','c','g','t'))
#self.gg_simdata.saveToNexusFile('doof.nex', self.taxon_labels, 'dna', ('a','c','g','t'))
#self.debugPAUPNexus(self.opts.out.postpred._getFilename(), core)
self._closePostPredFile()
if self.gg_bin_patterns:
# Compute the t function for the simulated dataset
curr_t = self.gg_simdata.calctBinned(4,self.minbins) # 4 = number of states
self.gg_binned_simdata = self.gg_simdata.getBinnedCounts()
if self.bincountsf is not None:
bstr = ['%.1f' % x for x in self.gg_binned_simdata]
self.bincountsf.write('%s\tposterior predictive replicate\n' % '\t'.join(bstr))
else:
# Compute the t function for the simulated dataset
curr_t = self.gg_simdata.calct(4)
# Add this value of t to the list (later the mean t will be computed)
self.gg_t.append(curr_t)
# Add the number of patterns in self.gg_simdata to the gg_npatterns list
self.gg_npatterns.append(self.gg_simdata.getNUniquePatterns())
# Update running mean vector gg_mu. A running mean is maintained because
# it is easy for the number of counts of constant patterns to overflow
# if you wait until the end of the MCMC run to divide by the total.
# Here is how the running mean is kept. Assume there will be four numbers
# (a, b, c, d) averaged. Thus, the desired quantity is (a+b+c+d)/4.
#
# gg_num_post_pred_reps self.gg_mu
# ------------------------------------------------------------
# 1 a = (a)/1
# 2 (1/2)a + b/2 = (a+b)/2
# 3 (2/3)[(a+b)/2] + c/3 = (a+b+c)/3
# 4 (3/4)[(a+b+c)/3] + d/4 = (a+b+c+d)/4
# ------------------------------------------------------------
#
# Note that it is ok if gg_num_post_pred_reps = 1 (in which case
# gg_mu is multiplied by zero). Because gg_mu is empty, multBy is
# a no-op in this case
p = 1.0/self.gg_num_post_pred_reps
not_p = 1.0 - p
self.gg_mu.multBy(not_p)
self.gg_simdata.multBy(p)
self.gg_simdata.addDataTo(self.gg_mu, 1.0)
# Increment count of the total number of simulated datasets created
# This value is used to later compute the mean t for all simulated datasets
# and the mean counts for all simulated data sets
self.gg_total += 1
self.ggCalculate()
if self.gg_bin_patterns and self.bincountsf is not None:
# write observed bin counts
bstr = ['%.1f' % x for x in self.gg_binned_y]
self.bincountsf.write('%s\tobserved\n' % '\t'.join(bstr))
# write mu bin counts
bstr = ['%.1f' % x for x in self.gg_binned_mu]
self.bincountsf.write('%s\tmu\n' % '\t'.join(bstr))
# write compromise action bin counts
for i,k in enumerate(self.opts.kvalues):
bstr = ['%.1f' % x for x in self.gg_a[i]]
self.bincountsf.write('%s\ta for k=%.1f\n' % ('\t'.join(bstr),k))
self._closeBinCountsFile()
return (self.gg_Pm, self.gg_Gm, self.gg_Dm);