def template_file(self): try: path=path_helpers.sanitize(self.path) except AttributeError: # fixme: self.name is always the name of the template file? path=path_helpers.sanitize("%s/%s/%s.%s" % (self.template_dir, self.type, self.name, self.suffix)) except TypeError: # sometimes self.path is None path=path_helpers.sanitize("%s/%s/%s.%s" % (self.template_dir, self.type, self.name, self.suffix)) self.path=path return path
def qsub_script(self, script_filename, out_filename=None, err_filename=None): if out_filename==None: out_filename=self.out_filename() if err_filename==None: err_filename=self.err_filename() qsub=templated(name='qsub', type='sh_template', suffix='tmpl') vars={} vars.update(self.__dict__) vars['name']=path_helpers.sanitize(self.name) vars['cmd']=script_filename vars['out_filename']=out_filename vars['err_filename']=err_filename qsub_script=qsub.eval_tmpl(vars=vars) qsub_script_file=path_helpers.sanitize(os.path.join(self.readset.working_dir, "%s.%s.qsub" % (self.name, self.readset.label))) f=open(qsub_script_file,"w") f.write(qsub_script) f.close() if RnaseqGlobals.conf_value('verbose'): print("%s written" % qsub_script_file) return qsub_script_file
def err_filename(self): return path_helpers.sanitize(os.path.join(self.readset.working_dir, "%s.err" % self.name))
def scriptname(self): return path_helpers.sanitize(os.path.join(self.working_dir(), '.'.join([self.name, self.readset.label, 'sh'])))