def runWorkflow_TestScript(sequences, newickTreeString,
batchSystem="single_machine",
buildAvgs=False, buildReference=False,
buildCactusPDF=False,
buildAdjacencyPDF=False,
makeCactusTreeStats=False,
makeMAFs=False,
configFile=None,
buildJobTreeStats=False):
"""Runs the workflow and various downstream utilities.
"""
#Setup the temp dir
tempDir = getTempDirectory(".")
logger.info("Using the temp dir: %s" % tempDir)
#Setup the output dir
outputDir = getTempDirectory(tempDir)
logger.info("Using the output dir: %s" % outputDir)
experiment = cactus.shared.test.runWorkflow_TestScript(sequences, newickTreeString,
outputDir=outputDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs, buildReference=buildReference,
configFile=configFile,
buildJobTreeStats=buildJobTreeStats)
cactusDiskDatabaseString = experiment.getDatabaseString()
#Run the cactus tree graph-viz plot
if buildCactusPDF:
cactusTreeDotFile = os.path.join(outputDir, "cactusTree.dot")
cactusTreePDFFile = os.path.join(outputDir, "cactusTree.pdf")
runCactusTreeViewer(cactusTreeDotFile, cactusDiskDatabaseString)
runGraphViz(cactusTreeDotFile, cactusTreePDFFile)
logger.info("Ran the cactus tree plot script")
else:
logger.info("Not building a cactus tree plot")
#Run the cactus tree graph-viz plot
if buildAdjacencyPDF:
adjacencyGraphDotFile = os.path.join(outputDir, "adjacencyGraph.dot")
adjacencyGraphPDFFile = os.path.join(outputDir, "adjacencyGraph.pdf")
runCactusAdjacencyGraphViewer(adjacencyGraphDotFile, cactusDiskDatabaseString)
#runGraphViz(adjacencyGraphDotFile, adjacencyGraphPDFFile) //Taking this line out to avoid graphviz crashing in an annoying way
logger.info("Ran the adjacency graph plot script")
else:
logger.info("Not building a adjacency graph plot")
if makeCactusTreeStats:
cactusTreeFile = os.path.join(outputDir, "cactusStats.xml")
runCactusTreeStats(cactusTreeFile, cactusDiskDatabaseString)
#Now run the latex script
statsFileTEX = os.path.join(outputDir, "cactusStats.tex")
runCactusTreeStatsToLatexTables([ cactusTreeFile ], [ "region0" ], statsFileTEX)
logger.info("Ran the tree stats script")
else:
logger.info("Not running cactus tree stats")
if makeMAFs:
mAFFile = os.path.join(outputDir, "cactus.maf")
runCactusMAFGenerator(mAFFile, cactusDiskDatabaseString)
logger.info("Ran the MAF building script")
else:
logger.info("Not building the MAFs")
#Now remove everything we generate
experiment.cleanupDatabase()
system("rm -rf %s" % tempDir)
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))
def runWorkflow_TestScript(sequences,
newickTreeString,
batchSystem="single_machine",
buildAvgs=False,
buildReference=False,
buildCactusPDF=False,
buildAdjacencyPDF=False,
makeCactusTreeStats=False,
makeMAFs=False,
configFile=None,
buildJobTreeStats=False):
"""Runs the workflow and various downstream utilities.
"""
#Setup the temp dir
tempDir = getTempDirectory(".")
logger.info("Using the temp dir: %s" % tempDir)
#Setup the output dir
outputDir = getTempDirectory(tempDir)
logger.info("Using the output dir: %s" % outputDir)
experiment = cactus.shared.test.runWorkflow_TestScript(
sequences,
newickTreeString,
outputDir=outputDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs,
buildReference=buildReference,
configFile=configFile,
buildJobTreeStats=buildJobTreeStats)
cactusDiskDatabaseString = experiment.getDatabaseString()
#Run the cactus tree graph-viz plot
if buildCactusPDF:
cactusTreeDotFile = os.path.join(outputDir, "cactusTree.dot")
cactusTreePDFFile = os.path.join(outputDir, "cactusTree.pdf")
runCactusTreeViewer(cactusTreeDotFile, cactusDiskDatabaseString)
runGraphViz(cactusTreeDotFile, cactusTreePDFFile)
logger.info("Ran the cactus tree plot script")
else:
logger.info("Not building a cactus tree plot")
#Run the cactus tree graph-viz plot
if buildAdjacencyPDF:
adjacencyGraphDotFile = os.path.join(outputDir, "adjacencyGraph.dot")
adjacencyGraphPDFFile = os.path.join(outputDir, "adjacencyGraph.pdf")
runCactusAdjacencyGraphViewer(adjacencyGraphDotFile,
cactusDiskDatabaseString)
#runGraphViz(adjacencyGraphDotFile, adjacencyGraphPDFFile) //Taking this line out to avoid graphviz crashing in an annoying way
logger.info("Ran the adjacency graph plot script")
else:
logger.info("Not building a adjacency graph plot")
if makeCactusTreeStats:
cactusTreeFile = os.path.join(outputDir, "cactusStats.xml")
runCactusTreeStats(cactusTreeFile, cactusDiskDatabaseString)
#Now run the latex script
statsFileTEX = os.path.join(outputDir, "cactusStats.tex")
runCactusTreeStatsToLatexTables([cactusTreeFile], ["region0"],
statsFileTEX)
logger.info("Ran the tree stats script")
else:
logger.info("Not running cactus tree stats")
if makeMAFs:
mAFFile = os.path.join(outputDir, "cactus.maf")
runCactusMAFGenerator(mAFFile, cactusDiskDatabaseString)
logger.info("Ran the MAF building script")
else:
logger.info("Not building the MAFs")
#Now remove everything we generate
experiment.cleanupDatabase()
system("rm -rf %s" % tempDir)
