def get_args(raw_args): parser = common.default_parser("Runs one of the prediction tools.") parser.add_argument("-t", "--tool", type=str, help="Prefix of one of the tools' names.") return parser.parse_args(raw_args)
def get_args(): parser = common.default_parser( "Get precision stats for a tool according to experimental data.") parser.add_argument("-t", "--tool", type=str, help="Prefix of one of the tools' names.") parser.add_argument( "-s", "--score", type=str, default=None, help="Name of the score to use (e.g. g20, doench_2014, decision, etc.)" ) parser.add_argument("--no_pam", action="store_true", help="Compare without PAM (should be used for mm10db)") parser.add_argument("--relative", action="store_true", help="Get precision based on relative scores") parser.add_argument( "--threshold", type=float, default=0, help="A threshold score above which a target is considered accepted") parser.add_argument( "--non_negative", action="store_true", help="Targets are accepted if and only if they have a non-negative " "score. Equivalent to setting the threshold at some negative " "epsilon.") return parser.parse_args()
def get_args(): parser = common.default_parser( "Creates an artificial genome from a dataset file.") parser.add_argument("-l", "--line_len", type=int, default=LINE_LEN, help="Length of lines in the output fasta file") parser.add_argument("-t", "--target_len", type=int, default=consts.TARGET_LEN, help="Length of target sequences") return parser.parse_args()
def get_args(raw_args): parser = common.default_parser( "Produces a fake refGene file for an artificial genome.") parser.add_argument( "-r", "--refgene", type=str, default=consts.REFGENE_FNAME, help="Name of output refGene file, with a single %%d for chr number") parser.add_argument("-t", "--target_len", type=int, default=consts.TARGET_LEN, help="Length of target sequences") return parser.parse_args(raw_args)
def get_args(raw_args): parser = common.default_parser( "Normalise the outputs of the supported prediction tools.") parser.add_argument("-t", "--tool", default=None, help="Prefix of one of the tools' names.") parser.add_argument( "-i", "--input", default=None, help="Path of input file (if not provided, the default input CSV of " "the dataset will be used)") parser.add_argument( "-o", "--output", default=None, help="Path of output file (if not provided, the default normalised " "output file will be used)") return parser.parse_args(raw_args)
def get_args(raw_args): parser = common.default_parser( "Samples targets from the GenomeCRISPR DB into CSV dataset file.") parser.set_defaults(dataset=DATASET_NAME) parser.add_argument("-s", "--size", type=int, default=1000, help="Number of targets to sample") parser.add_argument("-i", "--input", type=str, default=FULL_DATASET, help="Name of the full DB file") parser.add_argument( "-o", "--output", type=str, help=("Name of the output file. By default, the name is " "chr<chromosome number>_<sample size>.csv.")) return parser.parse_args(raw_args)
def get_args(): parser = common.default_parser("Runs SSC.") return parser.parse_args()
def get_args(): parser = common.default_parser("Runs FlashFry.") return parser.parse_args()
def get_args(): parser = common.default_parser( description="Returns the length of a chromosome sequence.") return parser.parse_args()
def get_args(): parser = common.default_parser( "Prepares the files and directories for a new dataset.", True) return parser.parse_args()
def get_args(): parser = common.default_parser( "Aggregates the outputs of all the tools for a specific dataset.") return parser.parse_args()
def get_args(): parser = common.default_parser("Runs sgRNA Scorer 2.0.") return parser.parse_args()
def get_args(): parser = common.default_parser( "Produces a features file for models to be trained on.") return parser.parse_args()
def get_args(): parser = common.default_parser("Runs phytoCRISP-Ex.") return parser.parse_args()