data_dir=self.data_dir) vcfFile.close() logMessage += "%s individuals, %s loci, md5sum=%s.\n" % ( no_of_individuals, no_of_loci, md5sum) else: logMessage += " is empty (no loci) or not VCF file.\n" self.outputLogMessage(logMessage) if self.commit: try: session.flush() session.commit() except: sys.stderr.write('Except type: %s\n' % repr(sys.exc_info())) import traceback traceback.print_exc() self.cleanUpAndExitOnFailure(exitCode=3) else: session.rollback() #delete all target files but exit gracefully (exit 0) self.cleanUpAndExitOnFailure(exitCode=0) if __name__ == '__main__': main_class = AddVCFFile2DB po = ProcessOptions(sys.argv, main_class.option_default_dict, error_doc=main_class.__doc__) instance = main_class(po.arguments, **po.long_option2value) instance.run()
def __init__(self, **keywords): """ 2011-7-12 """ self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \ class_to_have_attr=self)