def run(self):
logger.info('MergeTree object running, name: %s' % (self.name))
if self.nt is None:
return
for t in [self.nt.left, self.nt.right]:
if t is None:
continue
t.distance = 0.0
if not os.path.exists(os.path.join(self.options.simDir, lsc.nameTree(t), self.name + '.maf')):
sys.stderr.write('%s does not exist, recurse\n'
% os.path.join(self.options.simDir, lsc.nameTree(t), self.name+ '.maf'))
self.addChildTarget(MergeTree(t, self.nodeDict,
self.nodeParentDict, self.leafsDict, self.options))
else:
sys.stderr.write('%s does exist, don\'t recurse\n'
% os.path.join(self.options.simDir, lsc.nameTree(t),self.name + '.maf'))
self.setFollowOnTarget(MergeMafsDown(self.nt, self.nodeDict, self.nodeParentDict,
self.leafsDict, self.nodeParent, self.options))
def __init__(self, nt, nodeDict, nodeParentDict, leafsDict, options):
Target.__init__(self)
nt.distance = 0.0
self.nt = nt
self.name = lsc.nameTree(self.nt)
self.nodeDict = nodeDict
self.nodeParentDict = nodeParentDict
self.leafsDict = leafsDict
self.options = options
if self.name != self.options.rootName:
self.nodeParent = self.nodeParentDict[self.name]
else:
self.nodeParent = self.options.rootName
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)
