def main():
global CandidateCVlist
print("Eventscape %s" % xscape.PROGRAM_VERSION_TEXT)
hostTree, parasiteTree, phi, switchLo, switchHi, lossLo, lossHi, outfile = \
getInput.getInput(outputExtension ="csv")
while True:
merge_type = input("[U]nion or [I]ntersection? ")
if merge_type == "U" or merge_type == "I":
break
print("Invalid input. Please try again.")
CONFIG.intersection = merge_type == "I"
print("Reconciling trees...")
startTime = time.time()
print(" Preprocessing...")
preCVlist = reconcile.reconcile(parasiteTree, hostTree, phi, \
switchLo, switchHi, lossLo, lossHi)
CandidateCVlist.extend(restrict(preCVlist, \
switchLo, switchHi, lossLo, lossHi))
print(" Solving...")
CVlist = reconcileEvents(parasiteTree, hostTree, phi, \
switchLo, switchHi, lossLo, lossHi)
endTime = time.time()
elapsedTime = endTime- startTime
print("Elapsed time %.2f seconds" % elapsedTime)
output(outfile, CVlist, hostTree, switchLo, switchHi, lossLo, lossHi,
root=parasiteTree["pTop"][1])
print("Output written to file ", outfile)
def seqTrials(parasiteTree,
hostTree,
phi,
numTrials,
switchLo,
switchHi,
lossLo,
lossHi,
verbose=True):
''' Perform numTrials randomization trials sequentially. Although
parTrials could be used to do this too, this function doesn't
require the multiprocessing package and thus may be preferable
to some users in some situation.'''
parasiteTips, hostTips = getTipLists(parasiteTree, hostTree, phi)
output = []
for t in range(numTrials):
if verbose:
print(".", end=' ') # Progress indicator!
sys.stdout.flush()
newPhi = randomizeTips(parasiteTips, hostTips)
output.append(
reconcile.reconcile(parasiteTree, hostTree, newPhi, switchLo,
switchHi, lossLo, lossHi))
if verbose:
print() # Newline
return output
def parTrials(parasiteTree, hostTree, phi, numTrials, \
switchLo, switchHi, lossLo, lossHi, result,
verbose=True):
''' Perform numTrials randomization trials in one process. '''
parasiteTips, hostTips = getTipLists(parasiteTree, hostTree, phi)
output = []
for t in range(numTrials):
if verbose:
print(".", end=' ') # Progress indicator!
sys.stdout.flush()
newPhi = randomizeTips(parasiteTips, hostTips)
output.append(reconcile.reconcile(parasiteTree, hostTree, newPhi, \
switchLo, switchHi, lossLo, lossHi))
result.put(output)
def solve(newick_data, transferMin, transferMax, dupMin, dupMax, outfile, log):
print("Costscape %s" % xscape.PROGRAM_VERSION_TEXT)
hostTree = newick_data.host_dict
parasiteTree = newick_data.parasite_dict
tip_mapping = newick_data.tip_mapping
print("Reconciling trees...")
startTime = time.time()
CVlist = reconcile.reconcile(parasiteTree, hostTree, tip_mapping,
transferMin, transferMax, dupMin, dupMax)
endTime = time.time()
elapsedTime = endTime - startTime
print("Elapsed time %.2f seconds" % elapsedTime)
plotcosts.plotcosts(CVlist, transferMin, transferMax, dupMin, dupMax,
outfile, log)
if outfile is not None:
print("Output written to: ", outfile)
def solve(newick_data, transferMin, transferMax, dupMin, dupMax, optional):
print("Costscape %s" % xscape.PROGRAM_VERSION_TEXT)
hostTree, parasiteTree, phi, = newick_data
if optional.outfile == "":
display = True
else:
display = optional.display
print("Reconciling trees...")
startTime = time.time()
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, \
transferMin, transferMax, dupMin, dupMax)
endTime = time.time()
elapsedTime = endTime- startTime
print("Elapsed time %.2f seconds" % elapsedTime)
plotcosts.plotcosts(CVlist, transferMin, transferMax, dupMin, dupMax, \
optional.outfile, \
optional.log, display)
if optional.outfile != "":
print("Output written to file: ", optional.outfile)
def main():
print("Sigscape %s" % xscape.PROGRAM_VERSION_TEXT)
hostTree, parasiteTree, phi, switchLo, switchHi, lossLo, lossHi, \
outfile = getInput.getInput(outputExtension ="pdf", allowEmptyOutfile = True)
log = getInput.boolInput("Display in log coordinates? ")
if outfile == "":
display = True
else:
display = getInput.boolInput("Display to screen? ")
numTrials = getInput.intInput("Enter the number of randomization trials: ",
1)
numProcs = getInput.intInput(
"Enter the number of cores for parallelization: ", 1)
seed = getSeed("Enter random seed (leave blank if none): ")
if seed:
random.seed(seed)
print("Reconciling trees...")
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, \
switchLo, switchHi, lossLo, lossHi)
startTime = time.time()
if numProcs == 1:
randomTrialsCVlist = seqTrials(parasiteTree, hostTree, phi, \
numTrials,
switchLo, switchHi, \
lossLo, lossHi)
else:
randomTrialsCVlist = parallelTrials(parasiteTree, hostTree, phi, \
numTrials, numProcs, \
switchLo, switchHi, \
lossLo, lossHi)
endTime = time.time()
elapsedTime = endTime - startTime
print("\nElapsed time %.2f seconds" % elapsedTime)
print("Plotting...")
plotsig.plotsig(CVlist, randomTrialsCVlist, switchLo, switchHi, \
lossLo, lossHi, DOTS, outfile, \
log, display)
if outfile != "": print("Output written in file ", outfile)
