def saveIndexTree(self, supertreeSplits, supertreeDict):
for key, value in supertreeDict.items():
inter = Intersection(supertreeSplits[key][0],
supertreeSplits[key][1], 0, 0)
if self.doStandardDecoration:
self.csvValues.append([
key,
int(round(100.0 * (value[0] / self.T))),
int(round(100.0 * (value[1] / self.T))),
int(round(100.0 * (value[2] / self.T))),
int(round(100.0 * (value[3] / self.T))),
int(round(100.0 * (value[4] / self.T))),
int(round(100.0 * (value[5] / self.T))), value[6],
value[7], value[8], value[9], value[10], value[11]
])
else:
self.csvValues.append([
key, value[0] + value[1], value[0], value[1], value[2],
value[3], value[4], value[5], value[6], value[7], value[8],
value[9], value[10], value[11]
])
inter.name = str(key)
self.indexIntersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys,
self.taxnames)
self.indexSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(
self.indexIntersections, treeName='indexSupertree')
self.indexSuperTree.writeNexus(self.indexFilename)
writer = csv.writer(open(self.csvFilename, "wb"))
writer.writerows(self.csvValues)
def saveIndexTree(self, supertreeSplits, supertreeDict):
for key, value in supertreeDict.items():
inter = Intersection(supertreeSplits[key][0], supertreeSplits[key][1], 0, 0)
if self.doStandardDecoration:
self.csvValues.append(
[
key,
int(round(100.0 * (value[0] / self.T))),
int(round(100.0 * (value[1] / self.T))),
int(round(100.0 * (value[2] / self.T))),
int(round(100.0 * (value[3] / self.T))),
int(round(100.0 * (value[4] / self.T))),
int(round(100.0 * (value[5] / self.T))),
value[6],
value[7],
value[8],
value[9],
value[10],
value[11],
]
)
else:
self.csvValues.append(
[
key,
value[0] + value[1],
value[0],
value[1],
value[2],
value[3],
value[4],
value[5],
value[6],
value[7],
value[8],
value[9],
value[10],
value[11],
]
)
inter.name = str(key)
self.indexIntersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys, self.taxnames)
self.indexSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(
self.indexIntersections, treeName="indexSupertree"
)
self.indexSuperTree.writeNexus(self.indexFilename)
writer = csv.writer(open(self.csvFilename, "wb"))
writer.writerows(self.csvValues)
def buildDecoratedTree(self, supertreeSplits, supertreeDict):
for key, value in supertreeDict.items():
inter = Intersection(supertreeSplits[key][0], supertreeSplits[key][1], 0, 0)
name = ""
if self.doStandardDecoration:
name = str(int(round(100.0 * (1.0 + value[9]) / 2.0)))
else:
name = str(value[9])
inter.name = name
self.intersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys, self.taxnames)
self.decoratedSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(
self.intersections, treeName="decoratedSupertree"
)
def buildDecoratedTree(self, supertreeSplits, supertreeDict):
for key, value in supertreeDict.items():
inter = Intersection(supertreeSplits[key][0],
supertreeSplits[key][1], 0, 0)
name = ''
if self.doStandardDecoration:
name = str(int(round(100.0 * (1.0 + value[9]) / 2.0)))
else:
name = str(value[9])
inter.name = name
self.intersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys,
self.taxnames)
self.decoratedSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(
self.intersections, treeName='decoratedSupertree')