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()
