# If not in the main scripts directory, cd to the main scripts directory, if it exists. util.cdMainScriptsDirectory() # Process the command line arguments. scriptsDirectory = os.path.abspath(args.scriptsDirectory) inputDirectory = os.path.abspath(args.inputDirectory) outputDirectory = os.path.abspath(args.outputDirectory) stranded = args.stranded if (args.sort == "yes") | (args.sort == "yes"): sort = True else: sort = False # Check if the inputDirectory exists, and is a directory. util.checkInputDirectory(inputDirectory) # Read configuration files config = util.readConfigurationFiles() header = config.getboolean("server", "PBS_header") # Read samples file. Create file first if it doesn't exist. if not os.path.exists("samples.txt"): subprocess.call("samples.py", shell=True) samplesFile = pandas.read_csv("samples.txt", delim_whitespace=True) # Get samples conditions = samplesFile["group"] unique_conditions = list( OrderedDict.fromkeys(conditions)) # Remove duplicates.
"--submitJobsToQueue", help="Submit jobs to queue immediately.", choices=["yes", "no", "y", "n"], default="no") args = parser.parse_args() # If not in the main scripts directory, cd to the main scripts directory, if it exists. util.cdMainScriptsDirectory() # Process the command line arguments. scriptsDirectory = os.path.abspath(args.scriptsDirectory) inputDirectory = os.path.abspath(args.inputDirectory) outputDirectory = os.path.abspath(args.outputDirectory) # Check if the inputDirectory exists, and is a directory. util.checkInputDirectory(args.inputDirectory) # Read configuration files config = util.readConfigurationFiles() header = config.getboolean("server", "PBS_header") adapter = config.get("cutadapt", "adapter") minlength = config.get("cutadapt", "minimum-length") maxlength = config.get("cutadapt", "maximum-length") qualitycutoff = config.get("cutadapt", "quality-cutoff") trimn = config.getboolean("cutadapt", "trim-n") cut = config.get("cutadapt", "cut") tooshortoutput = config.getboolean("cutadapt", "tooshortoutput") toolongoutput = config.getboolean("cutadapt", "toolongoutput") # Create scripts directory, if it does not exist yet, and cd to it.
help="Submit jobs to queue immediately.", choices=["yes", "no", "y", "n"], default="no") args = parser.parse_args() # If not in the main scripts directory, cd to the main scripts directory, if it exists. util.cdMainScriptsDirectory() # Process the command line arguments. scriptsDirectory = os.path.abspath(args.scriptsDirectory) bamDirectory = os.path.abspath(args.bamDirectory) matsDirectory = os.path.abspath(args.matsDirectory) outputDirectory = os.path.abspath(args.outputDirectory) # Check if the bamDirectory exists, and is a directory. util.checkInputDirectory(bamDirectory) # Read configuration files config = util.readConfigurationFiles() header = config.getboolean("server", "PBS_header") toolsFolder = config.get("server", "toolsFolder") if config.has_option("rmats2sashimiplots", "comparisons"): comparisons = config.get("rmats2sashimiplots", "comparisons") else: comparisons = config.get("mats", "comparisons") # Read samples file. Create file first if it doesn't exist. if not os.path.exists("samples.txt"): subprocess.call("samples", shell=True)