Ejemplo n.º 1
0
    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))
Ejemplo n.º 2
0
 def run(self):
     analysisString = runCactusAnalyseAssembly(self.globalOutSequence)
     self.logToMaster("After preprocessing assembly we got the following stats: %s" % analysisString)