def __init__(self, thisNewickStr, thisParentDir, thisStepLength, options):
Target.__init__(self)
self.thisNewickStr = thisNewickStr
self.thisParentDir = thisParentDir
self.thisStepLength = thisStepLength
self.options = options
self.thisDir = lsc.treeStr2Dir(self.thisNewickStr, options.simDir)
self.theChild = os.path.basename(self.thisDir)
self.theParent = os.path.basename(self.thisParentDir)
def run(self):
logger.info('TreeFollow object running, %s' % self.thisGrandParentDir)
nt = newickTreeParser(self.thisNewickStr, 0.0)
name = lsc.nameTree(nt)
commonParentDir = os.path.abspath(os.path.join(self.options.simDir, name))
if nt.distance == 0:
if nt.internal:
# branch point
branches = { 'left' : lsc.tree2str(nt.left),
'right': lsc.tree2str(nt.right) }
for b in branches:
if not lsc.nodeIsLeaf(branches[b]):
self.addChildTarget(Tree(branches[b], commonParentDir, b, self.options))
childDir = lsc.treeStr2Dir(lsc.takeNewickStep(branches[b], self.options)[0],
self.options.simDir)
else:
# follow up to leaf cycles... Transalign and Stats only
self.setFollowOnTarget(LeafCleanUp(commonParentDir,
self.thisGrandParentDir, self.options))
else:
# stem with distance
self.addChildTarget(Tree(lsc.tree2str(nt), commonParentDir, 'stem', self.options))
childDir = lsc.treeStr2Dir(lsc.takeNewickStep(lsc.tree2str(nt), self.options)[0],
self.options.simDir)