def run(self, numThreads, outgroupSize):
# identify genes suitable for phylogenetic inference
print '--- Identifying genes suitable for phylogenetic inference ---'
genomeIds = self.inferGeneTrees(self.phyloUbiquity, self.phyloSingleCopy, numThreads, self.alignmentDir, self.hmmDir, outgroupSize)
# infer gene trees
print ''
print '--- Inferring gene trees ---'
makeTrees = MakeTrees()
makeTrees.run(self.alignmentDir, self.geneTreeDir, '.aln.masked.faa', numThreads)
# test gene trees for paralogs
print ''
print '--- Testing for paralogs in gene trees ---'
paralogTest = ParalogTest()
paralogTest.run(self.geneTreeDir, self.paralogAcceptPer, '.tre', self.conspecificGeneTreeDir)
# test gene trees for consistency with IMG taxonomy
print ''
print '--- Testing taxonomic consistency of gene trees ---'
consistencyTest = ConsistencyTest()
consistencyTest.run(self.conspecificGeneTreeDir, '.tre', self.consistencyAcceptPer, self.consistencyMinTaxa, self.consistencyOut, self.finalGeneTreeDir)
# gather phylogenetically informative HMMs into a single model file
print ''
print '--- Gathering phylogenetically informative HMMs ---'
getPhylogeneticHMMs = GetPhylogeneticHMMs()
getPhylogeneticHMMs.run(self.hmmDir, self.finalGeneTreeDir, self.phyloHMMsOut)
# infer genome tree
print ''
print '--- Inferring full genome tree ---'
inferGenomeTree = InferGenomeTree()
inferGenomeTree.run(self.finalGeneTreeDir, self.alignmentDir, '.aln.masked.faa', self.concatenatedAlignFile, self.treeOut, self.taxonomyOut, bSupportValues = True)
# replace IMG identifiers with ACE identifiers
imgIdToAceId = self.imgIdsToAceIds(genomeIds)
with open(self.treeOut) as f:
tree = ''.join(f.readlines())
for genomeId in genomeIds:
if genomeId in imgIdToAceId:
tree = tree.replace('IMG_' + genomeId, imgIdToAceId[genomeId])
fout = open(self.treeOutAce, 'w')
fout.write(tree)
fout.close()
def run(self, numThreads):
# identify genes suitable for phylogenetic inference
if False:
print(
'--- Identifying genes suitable for phylogenetic inference ---'
)
phylogeneticInferenceGenes = PhylogeneticInferenceGenes()
phylogeneticInferenceGenes.run(self.phyloUbiquity,
self.phyloSingleCopy, numThreads,
self.alignmentDir, self.hmmDir)
# infer gene trees
print('')
print('--- Inferring gene trees ---')
makeTrees = MakeTrees()
makeTrees.run(self.alignmentDir, self.geneTreeDir,
'.aln.masked.faa', numThreads)
# test gene trees for paralogs
print('')
print('--- Testing for paralogs in gene trees ---')
paralogTest = ParalogTest()
paralogTest.run(self.geneTreeDir, self.paralogAcceptPer, '.tre',
self.conspecificGeneTreeDir)
sys.exit()
# test gene trees for consistency with IMG taxonomy
print('')
print('--- Testing taxonomic consistency of gene trees ---')
consistencyTest = ConsistencyTest()
consistencyTest.run(self.conspecificGeneTreeDir, '.tre',
self.consistencyAcceptPer,
self.consistencyMinTaxa, self.consistencyOut,
self.finalGeneTreeDir)
# gather phylogenetically informative HMMs into a single model file
print('')
print('--- Gathering phylogenetically informative HMMs ---')
getPhylogeneticHMMs = GetPhylogeneticHMMs()
getPhylogeneticHMMs.run(self.hmmDir, self.finalGeneTreeDir,
self.phyloHMMsOut)
# infer genome tree
print('')
print('--- Inferring full genome tree ---')
inferGenomeTree = InferGenomeTree()
inferGenomeTree.run(self.finalGeneTreeDir, self.alignmentDir,
'.aln.masked.faa', self.concatenatedAlignFile,
self.treeOut, self.taxonomyOut)
# root genome tree between archaea and bacteria
print('')
print('--- Rooting full genome tree ---')
rerootTree = RerootTree()
rerootTree.run(self.treeOut, self.treeRootedOut)
# decorate genome tree with taxonomy using nlevel from tax2tree
print('')
print(
'--- Decorating full genome tree with taxonomic information using tax2tree ---'
)
os.system('t2t decorate -t %s -m %s -o %s' %
(self.treeRootedOut, self.taxonomyOut, self.treeTaxonomyOut))
if False:
# dereplicate identical sequences
print('')
print('--- Identifying duplicate sequences ---')
os.system(
'seqmagick convert --deduplicate-sequences --deduplicated-sequences-file '
+ self.derepSeqFile + ' ' + self.concatenatedAlignFile + ' ' +
self.derepConcatenatedAlignFile)
# infer dereplicated genome tree
print('')
print('--- Inferring dereplicated genome tree ---')
outputLog = self.treeDerepOut[0:self.treeDerepOut.rfind('.'
)] + '.log'
# cmd = 'FastTreeMP -nosupport -wag -gamma -log ' + outputLog + ' ' + self.derepConcatenatedAlignFile + ' > ' + self.treeDerepOut
cmd = 'FastTreeMP -wag -gamma -log ' + outputLog + ' ' + self.derepConcatenatedAlignFile + ' > ' + self.treeDerepOut
os.system(cmd)
# root genome tree between archaea and bacteria
print('')
print('--- Rooting dereplicated genome tree ---')
rerootTree = RerootTree()
rerootTree.run(self.treeDerepOut, self.treeDerepRootedOut)
# calculate bootstraps for genome tree
print('')
print('--- Calculating bootstrap support ---')
# bootstrapTree = BootstrapTree()
# bootstrapTree.run(self.bootstrapDir, self.treeDerepRootedOut, self.concatenatedAlignFile, 100, numThreads, self.treeDerepBootstrapOut)
# os.system('cp ' + self.treeDerepBootstrapOut + ' ' + self.treeDerepFinalOut)
# just use FastTree support values
os.system('cp ' + self.treeDerepRootedOut + ' ' +
self.treeDerepFinalOut)
# decorate dereplicated tree with unique IDs and a complementary file indicating properties of each internal node
print('')
print(
'--- Decorating final tree with lineage-specific statistics and marker set information ---'
)
decorateTree = DecorateTree()
decorateTree.decorate(self.treeTaxonomyOut, self.derepSeqFile,
self.treeDerepFinalOut, self.treeMetadata,
numThreads)
def run(self, numThreads, outgroupSize):
# identify genes suitable for phylogenetic inference
print '--- Identifying genes suitable for phylogenetic inference ---'
genomeIds = self.inferGeneTrees(self.phyloUbiquity,
self.phyloSingleCopy, numThreads,
self.alignmentDir, self.hmmDir,
outgroupSize)
# infer gene trees
print ''
print '--- Inferring gene trees ---'
makeTrees = MakeTrees()
makeTrees.run(self.alignmentDir, self.geneTreeDir, '.aln.masked.faa',
numThreads)
# test gene trees for paralogs
print ''
print '--- Testing for paralogs in gene trees ---'
paralogTest = ParalogTest()
paralogTest.run(self.geneTreeDir, self.paralogAcceptPer, '.tre',
self.conspecificGeneTreeDir)
# test gene trees for consistency with IMG taxonomy
print ''
print '--- Testing taxonomic consistency of gene trees ---'
consistencyTest = ConsistencyTest()
consistencyTest.run(self.conspecificGeneTreeDir, '.tre',
self.consistencyAcceptPer, self.consistencyMinTaxa,
self.consistencyOut, self.finalGeneTreeDir)
# gather phylogenetically informative HMMs into a single model file
print ''
print '--- Gathering phylogenetically informative HMMs ---'
getPhylogeneticHMMs = GetPhylogeneticHMMs()
getPhylogeneticHMMs.run(self.hmmDir, self.finalGeneTreeDir,
self.phyloHMMsOut)
# infer genome tree
print ''
print '--- Inferring full genome tree ---'
inferGenomeTree = InferGenomeTree()
inferGenomeTree.run(self.finalGeneTreeDir,
self.alignmentDir,
'.aln.masked.faa',
self.concatenatedAlignFile,
self.treeOut,
self.taxonomyOut,
bSupportValues=True)
# replace IMG identifiers with ACE identifiers
imgIdToAceId = self.imgIdsToAceIds(genomeIds)
with open(self.treeOut) as f:
tree = ''.join(f.readlines())
for genomeId in genomeIds:
if genomeId in imgIdToAceId:
tree = tree.replace('IMG_' + genomeId,
imgIdToAceId[genomeId])
fout = open(self.treeOutAce, 'w')
fout.write(tree)
fout.close()
def run(self, numThreads):
# identify genes suitable for phylogenetic inference
if False:
print '--- Identifying genes suitable for phylogenetic inference ---'
phylogeneticInferenceGenes = PhylogeneticInferenceGenes()
phylogeneticInferenceGenes.run(self.phyloUbiquity, self.phyloSingleCopy, numThreads, self.alignmentDir, self.hmmDir)
# infer gene trees
print ''
print '--- Inferring gene trees ---'
makeTrees = MakeTrees()
makeTrees.run(self.alignmentDir, self.geneTreeDir, '.aln.masked.faa', numThreads)
# test gene trees for paralogs
print ''
print '--- Testing for paralogs in gene trees ---'
paralogTest = ParalogTest()
paralogTest.run(self.geneTreeDir, self.paralogAcceptPer, '.tre', self.conspecificGeneTreeDir)
sys.exit()
# test gene trees for consistency with IMG taxonomy
print ''
print '--- Testing taxonomic consistency of gene trees ---'
consistencyTest = ConsistencyTest()
consistencyTest.run(self.conspecificGeneTreeDir, '.tre', self.consistencyAcceptPer, self.consistencyMinTaxa, self.consistencyOut, self.finalGeneTreeDir)
# gather phylogenetically informative HMMs into a single model file
print ''
print '--- Gathering phylogenetically informative HMMs ---'
getPhylogeneticHMMs = GetPhylogeneticHMMs()
getPhylogeneticHMMs.run(self.hmmDir, self.finalGeneTreeDir, self.phyloHMMsOut)
# infer genome tree
print ''
print '--- Inferring full genome tree ---'
inferGenomeTree = InferGenomeTree()
inferGenomeTree.run(self.finalGeneTreeDir, self.alignmentDir, '.aln.masked.faa', self.concatenatedAlignFile, self.treeOut, self.taxonomyOut)
# root genome tree between archaea and bacteria
print ''
print '--- Rooting full genome tree ---'
rerootTree = RerootTree()
rerootTree.run(self.treeOut, self.treeRootedOut)
# decorate genome tree with taxonomy using nlevel from tax2tree
print ''
print '--- Decorating full genome tree with taxonomic information using tax2tree ---'
os.system('t2t decorate -t %s -m %s -o %s' % (self.treeRootedOut, self.taxonomyOut, self.treeTaxonomyOut))
if False:
# dereplicate identical sequences
print ''
print '--- Identifying duplicate sequences ---'
os.system('seqmagick convert --deduplicate-sequences --deduplicated-sequences-file ' + self.derepSeqFile + ' ' + self.concatenatedAlignFile + ' ' + self.derepConcatenatedAlignFile)
# infer dereplicated genome tree
print ''
print '--- Inferring dereplicated genome tree ---'
outputLog = self.treeDerepOut[0:self.treeDerepOut.rfind('.')] + '.log'
# cmd = 'FastTreeMP -nosupport -wag -gamma -log ' + outputLog + ' ' + self.derepConcatenatedAlignFile + ' > ' + self.treeDerepOut
cmd = 'FastTreeMP -wag -gamma -log ' + outputLog + ' ' + self.derepConcatenatedAlignFile + ' > ' + self.treeDerepOut
os.system(cmd)
# root genome tree between archaea and bacteria
print ''
print '--- Rooting dereplicated genome tree ---'
rerootTree = RerootTree()
rerootTree.run(self.treeDerepOut, self.treeDerepRootedOut)
# calculate bootstraps for genome tree
print ''
print '--- Calculating bootstrap support ---'
# bootstrapTree = BootstrapTree()
# bootstrapTree.run(self.bootstrapDir, self.treeDerepRootedOut, self.concatenatedAlignFile, 100, numThreads, self.treeDerepBootstrapOut)
# os.system('cp ' + self.treeDerepBootstrapOut + ' ' + self.treeDerepFinalOut)
# just use FastTree support values
os.system('cp ' + self.treeDerepRootedOut + ' ' + self.treeDerepFinalOut)
# decorate dereplicated tree with unique IDs and a complementary file indicating properties of each internal node
print ''
print '--- Decorating final tree with lineage-specific statistics and marker set information ---'
decorateTree = DecorateTree()
decorateTree.decorate(self.treeTaxonomyOut, self.derepSeqFile, self.treeDerepFinalOut, self.treeMetadata, numThreads)