def run(self):
logger.info('MergeTreeFollow object running, name: %s' % (self.name))
outname = os.path.join(self.options.rootDir, 'burnin.maf')
if (os.path.exists(os.path.join(self.options.rootDir, 'burnin.tmp.maf'))
and not os.path.exists(outname)):
treelessRootCmd = ['-treelessRoot2=%s' % lsc.burninRootName(self.options)]
maf1 = os.path.join(self.options.rootDir, self.options.rootName + '.maf')
maf2 = os.path.join(self.options.rootDir, 'burnin.tmp.maf')
# drop = os.path.join(self.options.rootDir, 'burnin.dropped.maf')
cmds = lsc.buildMergeCommand(maf1, maf2, outname, treelessRootCmd,
self.name, self.options)
lsc.runCommands(cmds, self.getLocalTempDir())
def run(self):
logger.info('MergeMafsUp object running, name: %s nodeParent: %s'
% (self.name, self.nodeParent))
##############################
# The 'lookup' aspect of the merge is only performed when we are not at the root
# This merge merges the results of the 'lookdown' merge, that is to say the maf that contains
# all descendant sequences including the node, with the node-parent maf, to produce a maf
# that the parent can use to merge its children.
if self.name == self.options.rootName:
return
outname = os.path.join(self.options.simDir, self.name, self.nodeParent + '.maf')
if not os.path.exists(outname):
treelessRootCmd = ['-treelessRoot2=%s' % self.nodeParent]
maf1 = os.path.join(self.options.simDir, self.name, self.name + '.maf')
maf2 = os.path.join(self.options.simDir, self.name, self.nodeParent + '.tmp.maf')
cmds = lsc.buildMergeCommand(maf1, maf2, outname, treelessRootCmd,
self.name, self.options)
lsc.runCommands(cmds, self.getLocalTempDir())
def run(self):
logger.info('MergeTreeDown object running, name: %s nodeParent: %s'
% (self.name, self.nodeParent))
treelessRootCmd = []
for i in xrange(0,2):
if self.nodeDict[self.name].children[i] in self.leafsDict:
treelessRootCmd.append('-treelessRoot%d=%s' % (i + 1, self.name))
##############################
# the 'lookdown' aspect of the merge is performed for every node, including the root.
outname = os.path.join(self.options.simDir, self.name, self.name + '.maf')
if not os.path.exists(outname):
maf1 = os.path.join(self.options.simDir, self.nodeDict[self.name].children[0],
self.name + '.maf')
maf2 = os.path.join(self.options.simDir, self.nodeDict[self.name].children[1],
self.name + '.maf')
cmds = lsc.buildMergeCommand(maf1, maf2, outname, treelessRootCmd, self.name,
self.options)
lsc.runCommands(cmds, self.getLocalTempDir())
self.setFollowOnTarget(MergeMafsUp(self.nt, self.nodeDict, self.nodeParentDict,
self.leafsDict, self.nodeParent, self.options))
