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)
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)
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 )
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)
