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)
