def createfile(self, *arg, **params):
global file_dir
if not file_dir:
file_dir = ProfileFunc.GetBoxDisks(False)[0]
if params.get("docname"):
file_path = os.path.join(file_dir,params.get("docname"))
createFile(file_path,False,{'size':1})
return self.index(storages=file_dir)
# main
######################################################
print('Starting application...')
startTime = time.time()
globals.initialize() #Initialize the globals file
if globals.printToConsole:
print('Reading newick tree from file: %s...' % (newickFileName))
newickTree = Phylo.read(newickFileName, 'newick')
if globals.printToConsole:
Phylo.draw(newickTree)
globals.strains = strains #Assign pointer to the global strains array so we can access it anywhere
createFile(outputFileName, newickTree) #Creates file where data will be output
#Traverses the newick tree recursively reconstructing ancestral genomes
if globals.printToConsole:
print('Traversing newick tree...')
result = traverseNewickTree(newickTree.clade, None)
endTime = time.time()
totalTime = endTime - startTime
if globals.printToConsole:
#Output newick tree after the ancestors have been added to it
Phylo.draw(newickTree)
#Output ancestral genome to console
root = newickTree.clade
def main():
globals.initialize() #Initialize the globals file
global newickFileName
global outputFileName
global testFileName
if len(sys.argv) != 3:
print "WARNING: Must provide a Newick tree and test folder name. Exiting..."
sys.exit(0)
newickFileName = sys.argv[1]
if newickFileName == "tree2LeafNeighbour.dnd":
outputFileName = sys.argv[2] + "/ApplicationNeighbourOutput.txt"
else:
outputFileName = sys.argv[2] + "/ApplicationOutput.txt"
testFileName = sys.argv[2] + '/'
print('Starting application...')
startTime = time.time()
if globals.printToConsole:
print('Reading newick tree from file: %s...' % (newickFileName))
newickTree = Phylo.read(newickFileName, 'newick')
if globals.printToConsole:
Phylo.draw(newickTree)
globals.strains = strains #Assign pointer to the global strains array so we can access it anywhere
createFile(outputFileName,
newickTree) #Creates file where data will be output
#Traverses the newick tree recursively reconstructing ancestral genomes
if globals.printToConsole:
print('Traversing newick tree...')
result = traverseNewickTree(newickTree.clade, None)
endTime = time.time()
totalTime = endTime - startTime
#Output ancestral genome to console
if globals.printToConsole:
print('This is the root ancestral genome!')
root = newickTree.clade
rootGenome = []
if newickFileName == "tree2LeafNeighbour.dnd":
if len(root.clades) == 2:
child = root.clades[0]
if len(child.clades) != 2:
child = root.clades[1]
neighbour = root.clades[0]
else:
neighbour = root.clades[1]
if child.name != None and len(child.name) > 0:
filteredList = iter(
filter(lambda x: x.name == child.name, strains))
foundStrain = next(filteredList, None)
if foundStrain != None:
ancestralFragments = foundStrain.genomeFragments
rootGenome = ', '.join(fragment.originalSequence
for fragment in ancestralFragments)
with open(testFileName + "appNeighbourRoot.txt", "w+") as f:
f.write(rootGenome)
neighbour.name = ''
child.name = ''
else:
if root.name != None and len(root.name) > 0:
filteredList = iter(filter(lambda x: x.name == root.name, strains))
foundStrain = next(filteredList, None)
if foundStrain != None:
ancestralFragments = foundStrain.genomeFragments
rootGenome = ', '.join(fragment.originalSequence
for fragment in ancestralFragments)
with open(testFileName + "appRoot.txt", "w+") as f:
f.write(rootGenome)
if globals.printToConsole:
#Output newick tree after the ancestors have been added to it
Phylo.draw(newickTree)
#Need to traverse tree to ouput appropriate content to file
newickTree.clade.name = '' #Make sure that the output for the root is not output
traverseNewickTreeAndOutputToFile(newickTree.clade)
#Output the totals for the computation to console and file
outputTotalsToFile(outputFileName, totalTime)
#TODO compute lineage
#target = 'NC_014019'
#print('Computing lineage cost for: %s' % (target))
#lineageCost = computeLineageCost(newickTree.clade, target, None)
#if lineageCost != None:
#print('Successfully found and computed the lineage for: %s' % (target))
#Output Bar graphs of each event
if globals.printToConsole:
createBarGraph(globals.deletionSizeCounter,
'Distribution of Deletions')
createBarGraph(globals.duplicationSizeCounter,
'Distribution of Duplications')
createBarGraph(globals.inversionSizeDistributionCounter,
'Distribution of Inversions')
createBarGraph(globals.transpositionSizeDistributionCounter,
'Distribution of Transpositions')
createBarGraph(globals.invertedTranspositionSizeDistributionCounter,
'Distribution of Inverted Transpositions')
print('Total time (in seconds): %s' % (totalTime))
print('Ending application...')
#Case 3: Only the right sibling exists so return it
elif rightSibling != None and rightSibling.genomeFragments != None and len(
rightSibling.genomeFragments) > 0:
return rightSibling
#Case 4: None of the siblings exist so return NULL
else:
return None
######################################################
# main
######################################################
print('Starting application...')
startTime = time.time()
globals.initialize()
createFile(outputFileName) #Creates file where data will be output
print('Reading newick tree from file: %s...' % (newickFileName))
newickTree = Phylo.read(newickFileName, 'newick')
Phylo.draw(newickTree)
#Traverses the newick tree recursively reconstructing ancestral genomes
print('Traversing newick tree...')
result = traverseNewickTree(newickTree.clade, None)
endTime = time.time()
totalTime = endTime - startTime
print('Total time (in seconds): %s' % (totalTime))
print('Ending application...')
