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))