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'])))
