def getrmlsthelper(self):
        """
        Makes a system call to rest_auth.py, a Python script modified from
        https://github.com/kjolley/BIGSdb/tree/develop/scripts/test
        And downloads the most up-to-date rMLST profile and alleles
        """
        # Set the path/name of the folder to contain the new alleles and profile
        newfolder = os.path.join(self.path, self.analysistype)
        # Create the path
        make_path(newfolder)
        # Create arguments to feed into the rest_auth_class script
        args = ArgumentParser
        args.secret_file = os.path.join(self.credentials, 'secret.txt')
        args.file_path = os.path.join(self.credentials)
        args.output_path = newfolder
        args.logging = self.logging
        rmlst = rest_auth_class.REST(args)
        rmlst.secret_finder()
        rmlst.get_request_token()
        rmlst.get_access_token()
        # Download the profile and alleles
        rmlst.main()
        # Get the new alleles into a list, and create the combinedAlleles file
        alleles = glob(os.path.join(newfolder, '*.tfa'))
        self.combinealleles(newfolder, alleles)
def getrmlsthelper ( self ) : newfolder = os . path . join ( self . path , self . analysistype ) make_path ( newfolder ) args = ArgumentParser args . secret_file = os . path . join ( self . credentials , 'secret.txt' ) args . file_path = os . path . join ( self . credentials ) args . output_path = newfolder args . logging = self . logging rmlst = rest_auth_class . REST ( args ) rmlst . secret_finder ( ) rmlst . get_request_token ( ) rmlst . get_access_token ( ) rmlst . main ( ) alleles = glob ( os . path . join ( newfolder , '*.tfa' ) ) self . combinealleles ( newfolder , alleles )
Makes a system call to rest_auth.py, a Python script modified from
        https://github.com/kjolley/BIGSdb/tree/develop/scripts/test
        And downloads the most up-to-date rMLST profile and alleles