parser.add_argument("--cds", dest = "cdsFile", type = str, default = None,
help = "Input file containing CDS corresponding to input protein seqs")
parser.add_argument("--copy", dest = "copy", action = "store_false", default \
= True, help = "Avoid copying database and configuration files to the ROOT "
+ "folder")
## If no arguments are given, just show the help and finish
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
## Check whether the ROOT directory already exist or not ...
if lookForDirectory(args.outDir, False):
sys.exit(("ERROR: Output ROOT folder already exist '%s'") % (args.outDir))
args.outDir = os.path.abspath(args.outDir)
## ... and try to create it in case it doesn't exist
if not lookForDirectory(args.outDir, create = True):
sys.exit(("ERROR: ROOT folder '%s' cannot be created") % (args.outDir))
## Create folders to store the jobs file and (potentially) the configuration
## file and input databases
lookForDirectory(os.path.join(args.outDir, "jobs"))
lookForDirectory(os.path.join(args.outDir, "Data"))
lookForDirectory(os.path.join(args.outDir, "BlastDB"))
## Check parameters related to files / directories
if not lookForFile(os.path.abspath(args.script)):
if not lookForFile(args.dbFile):
sys.exit(("ERROR: Check input TARGET SEQUENCES file '%s' [Mode: HOMOLOGY "
+ "SEARCH]") % (args.dbFile))
parameters.setdefault("db_file", os.path.abspath(args.dbFile))
if args.cdsFile:
if not lookForFile(args.cdsFile):
sys.exit(("ERROR: Check input CDS file '%s'") % (args.cdsFile))
parameters.setdefault("cds", os.path.abspath(args.cdsFile))
if not lookForFile(args.configFile):
sys.exit(("ERROR: Check input CONFIG file '%s'") % (args.configFile))
parameters.setdefault("config_file", os.path.abspath(args.configFile))
if not lookForDirectory(args.outFolder):
sys.exit(("ERROR: Check output folder '%s'") % (args.outFolder))
parameters.setdefault("out_directory", os.path.abspath(args.outFolder))
## Set output files prefix name depending on input user selection
tag = os.path.split(args.inFile)[1].split(".")[0]
parameters.setdefault("prefix", args.prefix if args.prefix else tag)
## Read the other parameters from the input config file
parameters.update(readConfig(parameters["config_file"]))
## Check specific values for input parameters.
if not "coverage" in parameters or not (0.0 < float(parameters["coverage"]) \
<= 1.0):
sys.exit(("ERROR: Check your 'coverage' parameter"))