Пример #1
0
 def initialize_output(self):
     # Create the Output directory
     create_directory(self.output_dir)
     # Create a symbolic link from the data file to the output dir
     baseName = os.path.basename(self.input_file)
     symlinkPath = os.path.join(self.output_dir, baseName)
     if os.path.exists(symlinkPath):
         pass
     else:
         absPath = os.path.abspath(self.input_file)
         os.symlink(absPath, symlinkPath)
     self.sequenceFile = baseName
     # Move into the Output directory and create Log directory and files
     os.chdir(self.output_dir)
     create_directory('log')
     stdoutLog = os.path.join('log', 'mothur_stdout.log')
     stderrLog = os.path.join('log', 'mothur_stderr.log')
     self.log_file = os.path.join('log', 'rna_pipeline.log')
     # Instantiate the MothurRunner object
     self.factory = MothurRunner(self.mothur, self.nproc, stdoutLog,
                                 stderrLog)
Пример #2
0
 def initialize_output(self):
     # Create the Output directory
     create_directory( self.output_dir )
     # Create a symbolic link from the data file to the output dir
     baseName = os.path.basename( self.input_file )
     symlinkPath = os.path.join( self.output_dir, baseName )
     if os.path.exists( symlinkPath ):
         pass
     else:
         absPath = os.path.abspath( self.input_file )
         os.symlink( absPath, symlinkPath )
     self.sequenceFile = baseName
     # Move into the Output directory and create Log directory and files
     os.chdir( self.output_dir )
     create_directory( 'log' )
     stdoutLog = os.path.join('log', 'mothur_stdout.log')
     stderrLog = os.path.join('log', 'mothur_stderr.log')
     self.log_file = os.path.join('log', 'rna_pipeline.log')
     # Instantiate the MothurRunner object
     self.factory = MothurRunner( self.mothur, 
                                  self.nproc, 
                                  stdoutLog, 
                                  stderrLog)
Пример #3
0
 def initializeOutputFolder( self ):
     # Create the output directory if needed and move into it
     self.origin=   os.getcwd()
     create_directory( self.outputDir )
     os.chdir( self.outputDir )
Пример #4
0
 def initializeOutputFolder(self):
     # Create the output directory if needed and move into it
     self.origin = os.getcwd()
     create_directory(self.outputDir)
     os.chdir(self.outputDir)