def __init__(self): RunCommand.__init__(self, args_usage="<variants-file> [<variants-file> ...]", epilog=PROJECT_EPILOG) self.variants_files = [] # Gather variants files from arguments for var_file in self.args.files: if not os.path.isabs(var_file): var_file = os.path.join(os.getcwd(), var_file) if not os.path.exists(var_file): self.log.error("Variants file not found: {}".format(var_file)) exit(-1) if not os.path.isfile(var_file): self.log.error("A file is expected: {}".format(var_file)) exit(-1) self.variants_files += [var_file] # Get project id if self.args.project_id is None: self.log.error("Project identifier not specified.") exit(-1) self.project_id = normalize_id(self.args.project_id)
def process_conf(self): RunCommand.process_conf(self) if "workflows_path" not in self.conf: self.conf_builder.add_value("workflows_path", self.workflows_path) if "results_path" not in self.conf: self.conf_builder.add_value("results_path", self.results_path) if "temp_path" not in self.conf: self.conf_builder.add_value("temp_path", self.temp_path)
def build_conf(self): if self.case_name is None: self.case_name = self.project_id RunCommand.build_conf(self) self.case_conf_builder.add_value("project.id", self.project_id) if self.args.single_tumor: self.case_conf_builder.add_value("variants_only", True) self.case_conf_builder.add_value("skip_oncodrivefm", True) self.case_conf_builder.add_value("skip_oncodriveclust", True)
def add_arguments(self, parser): RunCommand.add_arguments(self, parser) parser.add_argument("files", nargs="+", help="Variants files") parser.add_argument("-p", "--id", dest="project_id", metavar="NAME", help="Define the project identifier. Required.") parser.add_argument("-a", "--assembly", dest="assembly", metavar="ASSEMBLY", choices=["hg18", "hg19"], default="hg19", help="Define the assembly [hg18, hg19]. Default is hg19.") parser.add_argument("--single-tumor", dest="single_tumor", action="store_true", default=False, help="Run a single tumor analysis instead of the regular cohort analysis.")
def __init__(self): RunCommand.__init__(self, args_usage = "<projects-path> [<projects-path> ...]", epilog = PROJECT_EPILOG) self.scan_paths = [] # Gather scan paths from arguments for scan_path in self.args.paths: if not os.path.isabs(scan_path): scan_path = os.path.join(os.getcwd(), scan_path) if not os.path.exists(scan_path): self.log.error("Path not found: {}".format(scan_path)) exit(-1) self.scan_paths += [scan_path]
def add_arguments(self, parser): RunCommand.add_arguments(self, parser) parser.add_argument("paths", nargs="+", help="Projects paths") parser.add_argument("-i", "--include", dest = "include", metavar = "ID", action="append", help = "Include project which id=ID") parser.add_argument("-I", "--include-regex", dest = "include_regex", metavar = "REGEX", action="append", help = "Include project which id matches REGEX") parser.add_argument("--include-from", dest = "include_from", metavar = "FILE", action="append", help = "Include project which id found in file FILE") parser.add_argument("-e", "--exclude", dest = "exclude", metavar = "ID", action="append", help = "Exclude project which id=ID") parser.add_argument("-E", "--exclude-regex", dest = "exclude_regex", metavar = "REGEX", action="append", help = "Exclude project which id matches REGEX") parser.add_argument("--exclude-from", dest = "exclude_from", metavar = "FILE", action="append", help = "Exclude project which id found in file FILE")
def __init__(self): RunCommand.__init__(self, args_usage="<projects-path> [<projects-path> ...]", epilog=PROJECT_EPILOG)
def build_conf(self): RunCommand.build_conf(self)