def run(self):
# If the files are in a sub-dir then rip them out.
if os.path.isdir(self.inputSequenceFileOrDirectory):
tempFile = getTempFile(rootDir=self.getGlobalTempDir())
catFiles(
[
os.path.join(self.inputSequenceFileOrDirectory, f)
for f in os.listdir(self.inputSequenceFileOrDirectory)
],
tempFile,
)
inputSequenceFile = tempFile
else:
inputSequenceFile = self.inputSequenceFileOrDirectory
assert inputSequenceFile != self.outputSequenceFile
prepXmlElems = self.configNode.findall("preprocessor")
analysisString = runCactusAnalyseAssembly(inputSequenceFile)
self.logToMaster(
"Before running any preprocessing on the assembly: %s got following stats (assembly may be listed as temp file if input sequences from a directory): %s"
% (self.inputSequenceFileOrDirectory, analysisString)
)
if len(prepXmlElems) == 0: # Just cp the file to the output file
system("cp %s %s" % (inputSequenceFile, self.outputSequenceFile))
else:
logger.info("Adding child batch_preprocessor target")
self.addChildTarget(BatchPreprocessor(prepXmlElems, inputSequenceFile, self.outputSequenceFile, 0))
def run(self):
analysisString = runCactusAnalyseAssembly(self.globalOutSequence)
self.logToMaster("After preprocessing assembly we got the following stats: %s" % analysisString)