# 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)
