def getInput(outputExtension, allowEmptyOutfile=False):
""" outputExtension is the output file extension (e.g, pdf or csv) """
# Get input file name and try to open it
# while True:
# fileName = raw_input("Enter .newick input file name: ")
# if fileName.endswith(".newick"):
# try:
# fileHandle = open(fileName, 'r')
# break
# except IOError:
# print "Error reading file. Please try again."
# else:
# print "File name must end in .newick. Please try again."
fileHandle = open("/Users/hmcguest/Downloads/xscape/examples/heliconius.newick", "r")
hostTree, parasiteTree, phi = newickFormatReader(fileHandle)
fileHandle.close()
# Get output file name
# while True:
# if allowEmptyOutfile:
# outfile = raw_input("Enter ." + outputExtension + " name for output file (or Return): ")
# if outfile == "": break
# else:
# outfile = raw_input("Enter ." + outputExtension + " name for output file: ")
# if outfile.endswith(outputExtension):
# break
# else:
# print "File name must end in ." + outputExtension + ". Please try again."
# Get parameter value ranges
outfile = "out.pdf"
# switchLo = floatInput("Enter switch low value: ", min_val=0.9)
# switchHi = floatInput("Enter switch high value: ", min_val=1.2)
# lossLo = floatInput("Enter loss low value: ", min_val=0.9)
# lossHi = floatInput("Enter loss high value: ", min_val=1.2)
switchLo = 0.9
switchHi = 1.2
lossLo = 0.9
lossHi = 1.2
return hostTree, parasiteTree, phi, switchLo, switchHi, lossLo, lossHi, outfile
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 getInput(outputExtension, allowEmptyOutfile=False):
""" outputExtension is the output file extension (e.g, pdf or csv) """
# Get input file name and try to open it
while True:
fileName = raw_input("Enter .newick input file name: ")
if fileName.endswith(".newick"):
try:
fileHandle = open(fileName, 'r')
break
except IOError:
print "Error reading file. Please try again."
else:
print "File name must end in .newick. Please try again."
hostTree, parasiteTree, phi = newickFormatReader(fileHandle)
fileHandle.close()
# Get output file name
while True:
if allowEmptyOutfile:
outfile = raw_input("Enter ." + outputExtension +
" name for output file (or Return): ")
if outfile == "": break
else:
outfile = raw_input("Enter ." + outputExtension +
" name for output file: ")
if outfile.endswith(outputExtension):
break
else:
print "File name must end in ." + outputExtension + ". Please try again."
# Get parameter value ranges
switchLo = floatInput("Enter switch low value: ", min_val=0)
switchHi = floatInput("Enter switch high value: ", min_val=switchLo)
lossLo = floatInput("Enter loss low value: ", min_val=0)
lossHi = floatInput("Enter loss high value: ", min_val=lossLo)
return hostTree, parasiteTree, phi, switchLo, switchHi, lossLo, lossHi, 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 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 getInput(outputExtension, allowEmptyOutfile=False):
""" outputExtension is the output file extension (e.g, pdf or csv) """
# Get input file name and try to open it
while True:
fileName = raw_input("Enter .newick input file name: ")
if fileName.endswith(".newick"):
try:
fileHandle = open(fileName, 'r')
break
except IOError:
print "Error reading file. Please try again."
else:
print "File name must end in .newick. Please try again."
hostTree, parasiteTree, phi = newickFormatReader(fileHandle)
fileHandle.close()
# Get output file name
while True:
if allowEmptyOutfile:
outfile = raw_input("Enter ." + outputExtension + " name for output file (or Return): ")
if outfile == "": break
else:
outfile = raw_input("Enter ." + outputExtension + " name for output file: ")
if outfile.endswith(outputExtension):
break
else:
print "File name must end in ." + outputExtension + ". Please try again."
# Get parameter value ranges
switchLo = floatInput("Enter switch low value: ", min_val=0)
switchHi = floatInput("Enter switch high value: ", min_val=switchLo)
lossLo = floatInput("Enter loss low value: ", min_val=0)
lossHi = floatInput("Enter loss high value: ", min_val=lossLo)
return hostTree, parasiteTree, phi, switchLo, switchHi, lossLo, lossHi, outfile