def run(self):
previousOutputFile = None
previousOutputFile2 = None
blanchettePath = os.path.join(TestStatus.getPathToDataSets(), "blanchettesSimulation")
for i in xrange(self.options.blanchetteRepeats):
trueAlignmentMFA = os.path.join(os.path.join(blanchettePath, "%.2i.job" % i), "true.mfa")
trueAlignmentMAF = os.path.join(self.getLocalTempDir(), "temp.maf")
treeFile = os.path.join(blanchettePath, "tree.newick")
system("mfaToMaf --mfaFile %s --outputFile %s --treeFile %s" % (trueAlignmentMFA, trueAlignmentMAF, treeFile))
trueRenamedMAF = trueAlignmentMAF + ".renamed"
expPath = os.path.join(self.outputDir, str(i), "experiment.xml")
applyNamingToMaf(expPath, trueAlignmentMAF, trueRenamedMAF)
trueAlignmentMAF = trueRenamedMAF
if self.params.vanilla == False:
predictedAlignmentMaf = os.path.join(self.outputDir, str(i), "progressiveCactusAlignment", "Anc0", "Anc0.maf")
else:
predictedAlignmentMaf = os.path.join(self.outputDir, str(i), "cactusVanilla.maf")
outputFile = os.path.join(self.getLocalTempDir(), "temp%i" % i)
system("mafComparator --mafFile1 %s --mafFile2 %s --outputFile %s" % (trueAlignmentMAF, predictedAlignmentMaf, outputFile))
system("cp %s %s" % (outputFile, os.path.join(self.outputDir, str(i), "mafComparison.xml")))
if previousOutputFile != None:
system("mergeMafComparatorResults.py --results1 %s --results2 %s --outputFile %s" % (outputFile, previousOutputFile, outputFile))
previousOutputFile = outputFile
system("mv %s %s" % (previousOutputFile, os.path.join(self.outputDir, "mafComparison.xml")))
def run(self):
if not os.path.exists(self.outputFile):
outputFile = os.path.join(self.getLocalTempDir(), "temp.xml")
trueRenamedMAF = os.path.join(self.getLocalTempDir(), "true_renamed.maf")
outputDir = os.path.split(self.outputFile)[0]
expPath = os.path.join(outputDir, "experiment.xml")
applyNamingToMaf(expPath, self.trueMaf, trueRenamedMAF)
self.trueMaf = trueRenamedMAF
system("mafComparator --mafFile1 %s --mafFile2 %s --outputFile %s" % (self.trueMaf, self.predictedMaf, outputFile))
system("mv %s %s" % (outputFile, self.outputFile))
