def runProgressive(self):
logger.debug("Going to put the alignment in %s" % self.outputDir)
if not os.path.isdir(self.outputDir):
os.mkdir(self.outputDir)
if not os.path.exists(os.path.join(self.outputDir, "progressiveCactusAlignment")):
xmlTree = ET.parse(os.path.join(getRootPathString(), "lib", "cactus_workflow_config.xml"))
#Set the parameters
tempLocalDir = os.path.join(self.outputDir, "tempProgressiveCactusAlignment")
system("rm -rf %s" % tempLocalDir)
os.mkdir(tempLocalDir)
#Set the config parameters
self.params.applyToXml(xmlTree)
config = xmlTree.getroot()
assert config is not None
#Write the config file
tempConfigFile = os.path.join(tempLocalDir, "config.xml")
fileHandle = open(tempConfigFile, 'w')
assert fileHandle is not None
tree = ET.ElementTree(config)
tree.write(fileHandle)
fileHandle.close()
#Make the experiment file
tempExperimentFile = os.path.join(tempLocalDir, "experiment.xml")
if self.params.kyotoTycoon == True:
dbConfElem = ET.Element("st_kv_database_conf", type="kyoto_tycoon")
ktElem = ET.SubElement(dbConfElem, "kyoto_tycoon", host="localhost", port="1978", database_dir="dummy")
else:
dbConfElem = None
cactusWorkflowExperiment = CactusWorkflowExperiment(
sequences=self.sequences,
newickTreeString=self.newickTree,
#requiredSpecies=self.requiredSpecies,
#singleCopySpecies=self.singleCopySpecies,
databaseName="cactusAlignment",
outputDir=tempLocalDir,
configFile=tempConfigFile,
databaseConf = dbConfElem)
cactusWorkflowExperiment.writeExperimentFile(tempExperimentFile)
#The jobtree
tempJobTreeDir = os.path.join(tempLocalDir, "jobTree")
#The place to put the temporary experiment dir
tempExperimentDir = os.path.join(tempLocalDir, "progressiveCactusAlignment")
#The temporary experiment
runCactusCreateMultiCactusProject(tempExperimentFile,
tempExperimentDir)
logger.info("Setup the cactus progressive experiment")
runCactusProgressive(os.path.join(tempExperimentDir, "progressiveCactusAlignment_project.xml"),
tempJobTreeDir,
#batchSystem=batchSystem,
buildMaf=True,
joinMaf=True,
#buildTrees=buildTrees, buildFaces=buildFaces, buildReference=buildReference,
jobTreeStats=True,
maxThreads=4,
logLevel="DEBUG")
logger.info("Ran the progressive workflow")
#Check if the jobtree completed sucessively.
runJobTreeStatusAndFailIfNotComplete(tempJobTreeDir)
logger.info("Checked the job tree dir for the progressive run")
#Run the cactus tree stats
expPath = os.path.join(tempExperimentDir, "Anc0", "Anc0_experiment.xml")
exp = ExperimentWrapper(ET.parse(expPath).getroot())
if exp.getDbType() == "kyoto_tycoon":
ktserver = KtserverLauncher()
ktserver.spawnServer(exp)
treeStatsFile = os.path.join(self.outputDir, "treeStats.xml")
system("cactus_treeStats --cactusDisk \'%s\' --flowerName 0 --outputFile %s" %(exp.getDiskDatabaseString(),
treeStatsFile))
if exp.getDbType() == "kyoto_tycoon":
ktserver.killServer(exp)
#Now copy the true assembly back to the output
system("mv %s %s/experiment.xml" % (tempExperimentFile, self.outputDir))
system("mv %s %s" % (tempExperimentDir, self.outputDir))
system("jobTreeStats --jobTree %s --outputFile %s/jobTreeStats.xml" % (tempJobTreeDir, self.outputDir))
system("mv %s %s/config.xml" % (tempConfigFile, self.outputDir))
#But keep a link to the multicactus project in its original path so we can navigate
# the paths in the xml...
actualResultsDir = os.path.join(os.path.abspath(self.outputDir), "progressiveCactusAlignment")
tempResultsDir = os.path.join(self.outputDir, "tempProgressiveCactusAlignment")
system("ln -s %s %s" % (actualResultsDir, tempResultsDir))
def runVanilla(self):
logger.debug("Going to put the alignment in %s" % self.outputDir)
if not os.path.isdir(self.outputDir):
os.mkdir(self.outputDir)
if not os.path.exists(os.path.join(self.outputDir, "cactusAlignmentVanilla")):
xmlTree = ET.parse(os.path.join(getRootPathString(), "lib", "cactus_workflow_config.xml"))
#Set the parameters
tempLocalDir = os.path.join(self.outputDir, "tempVanillaCactusAlignment")
system("rm -rf %s" % tempLocalDir)
os.mkdir(tempLocalDir)
#Set the config parameters
self.params.applyToXml(xmlTree)
config = xmlTree.getroot()
assert config is not None
#Write the config file
tempConfigFile = os.path.join(tempLocalDir, "config.xml")
fileHandle = open(tempConfigFile, 'w')
assert fileHandle is not None
tree = ET.ElementTree(config)
tree.write(fileHandle)
fileHandle.close()
#Make the experiment file
tempExperimentFile = os.path.join(tempLocalDir, "experiment.xml")
#Now do standard cactus..
#Make the experiment file
tempExperimentFile2 = os.path.join(tempLocalDir, "experiment.xml")
cactusWorkflowExperiment = CactusWorkflowExperiment(
sequences=self.sequences,
newickTreeString=self.newickTree,
#requiredSpecies=self.requiredSpecies,
#singleCopySpecies=self.singleCopySpecies,
databaseName="cactusAlignmentVanilla",
outputDir=tempLocalDir,
configFile=tempConfigFile)
tempExperimentDir2 = os.path.join(tempLocalDir, "cactusAlignmentVanilla")
cactusWorkflowExperiment.writeExperimentFile(tempExperimentFile2)
# apply naming to the event tree to be consistent with progressive
exp = ExperimentWrapper(ET.parse(tempExperimentFile2).getroot())
cleanEventTree(exp)
exp.writeXML(tempExperimentFile2)
#We're done with the progressive, now run the vanilla cactus for comparison
tempJobTreeDir2 = os.path.join(tempLocalDir, "jobTreeVanilla")
runCactusWorkflow(tempExperimentFile2, tempJobTreeDir2,
jobTreeStats=True,
setupAndBuildAlignments=True,
buildReference=True,
maxThreads=4)
runJobTreeStatusAndFailIfNotComplete(tempJobTreeDir2)
logger.info("Checked the job tree dir for the vanilla run")
runCactusMAFGenerator(os.path.join(self.outputDir, "cactusVanilla.maf"), getCactusDiskString(tempExperimentDir2))
#Run the cactus tree stats
treeStatsFile = os.path.join(self.outputDir, "treeStats.xml")
system("cactus_treeStats --cactusDisk \'%s\' --flowerName 0 --outputFile %s" %(exp.getDiskDatabaseString(),
treeStatsFile))
system("jobTreeStats --jobTree %s --outputFile %s/jobTreeStats.xml" % (tempJobTreeDir2, self.outputDir))
system("mv %s %s" % (tempExperimentDir2, self.outputDir))
system("mv %s %s/experiment.xml" % (tempExperimentFile2, self.outputDir))