def _check_args(self):
Command._check_args(self)
if self.args.analysis_name is None:
names = [os.path.splitext(os.path.basename(path))[0] for path in self.args.data_paths]
prefix = os.path.commonprefix(names)
if prefix.endswith("-"):
prefix = prefix[:-1]
if len(prefix) == 0:
prefix = "oncodrivefm"
self.args.analysis_name = prefix
def _check_args(self):
Command._check_args(self)
if self.args.analysis_name is None:
self.args.analysis_name, ext = os.path.splitext(os.path.basename(self.args.data_path))
if self.args.num_samplings < 1:
self._error("Number of samplings out of range [2, ..)")
if self.args.mut_threshold < 1:
self._error("Minimum number of mutations out of range [1, ..)")
if self.args.filter is not None:
if not os.path.exists(self.args.filter):
self._error("Filter file not found: {0}".format(self.args.filter))
def _check_args(self):
Command._check_args(self)
if self.args.analysis_name is None:
self.args.analysis_name, ext = os.path.splitext(os.path.basename(self.args.data_path))
if self.args.num_samplings < 1:
self._error("Number of samplings out of range [2, ..)")
if self.args.mut_gene_threshold < 1:
self._error("Minimum number of mutations per gene out of range [1, ..)")
if self.args.mut_pathway_threshold < 1:
self._error("Minimum number of mutations per pathway out of range [1, ..)")
if self.args.mapping is not None and not os.path.isfile(self.args.mapping):
self._error("Pathways mapping file not found: {0}".format(self.args.mapping))
