def findCenters(newickFile, switchLo, switchHi, lossLo, lossHi):
"""This function takes as input a .newick file in the form
<filename>.newick, and low and high values for costscape for both
switches and losses. It returns a list of the centroids of each region in
the costscape associated with the given .newick file."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo,
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo,
switchHi, "", False, False)
polygonList = getNewCoordList(newickFile, switchLo, switchHi, lossLo,
lossHi)
pointList = []
for i in range(len(polygonList)):
point = polygonList[i]
numCommas = point.count(",")
if numCommas > 1:
# polygon case
region = load_wkt(point)
pointList.append(region.centroid.wkt)
elif numCommas == 1:
# line case
x1 = coordList[i][0][0]
y1 = coordList[i][0][1]
x2 = coordList[i][1][0]
y2 = coordList[i][1][1]
midx = (x1 + x2) * 1.0 / 2
midy = (y1 + y2) * 1.0 / 2
pointList.append("POINT ({} {})".format(str(midx), str(midy)))
else:
# point case
pointList.append("POINT {}".format(str(coordList[i][0])))
return pointList
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 getNewCoordList(newickFile, switchLo, switchHi, lossLo, lossHi):
"""Takes as input a newick file in the form <filename>.newick, and low
and high values for costscape for both switches and losses. Returns a
list of strings, where each string contains all the verteces of one
region from costscape."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo,
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo,
switchHi, "", False, False)
newCoordList = []
for vertexList in coordList:
string = "POLYGON(("
for vertex in vertexList:
string = "{}{} {},".format(string, str(vertex[0]), str(vertex[1]))
string = "{}))".format(string[:-1])
newCoordList.append(string)
return newCoordList
def getNewCoordList(newickFile, switchLo, switchHi, lossLo, lossHi):
"""Takes as input a newick file in the form <filename>.newick, and low
and high values for costscape for both switches and losses. Returns a
list of strings, where each string contains all the verteces of one
region from costscape."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo, \
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo, \
switchHi, "", False, False)
newCoordList = []
for element in coordList:
string = "POLYGON(("
for i in element:
string = string + str(i[0]) + ' ' + str(i[1]) + ','
string = string[:-1] + '))'
newCoordList.append(string)
return newCoordList
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)
def solve(newick_data, switchLo, switchHi, lossLo, lossHi, 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, \
switchLo, switchHi, lossLo, lossHi)
endTime = time.time()
elapsedTime = endTime - startTime
print("Elapsed time %.2f seconds" % elapsedTime)
plotcosts.plotcosts(CVlist, switchLo, switchHi, lossLo, lossHi, \
optional.outfile, \
optional.log, display)
if optional.outfile != "":
print("Output written to file: ", optional.outfile)
def findCenters(newickFile, switchLo, switchHi, lossLo, lossHi):
"""This function takes as input a .newick file in the form
<filename>.newick, and low and high values for costscape for both
switches and losses. It returns a list of the centroids of each region in
the costscape associated with the given .newick file."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo, \
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo, \
switchHi, "", False, False)
polygonList = getNewCoordList(newickFile, switchLo, switchHi, lossLo, \
lossHi)
pointList = []
for i in range(len(polygonList)):
point = polygonList[i]
numCommas = 0
for j in range(len(point)):
if point[j] == ",":
numCommas = numCommas + 1
if numCommas > 1:
#polygon case
region = load_wkt(point)
pointList.append((region.centroid.wkt))
elif numCommas == 1:
#line case
x1 = coordList[i][0][0]
y1 = coordList[i][0][1]
x2 = coordList[i][1][0]
y2 = coordList[i][1][1]
midx = (x1 + x2) * 1.0 / 2
midy = (y1 + y2) * 1.0 / 2
pointList.append("POINT (" + str(midx) + " " + str(midy) + ")")
else:
#point case
pointList.append("POINT " + str(coordList[i][0]))
return pointList
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)