This actually runs the qvality program from PATH.

def write(self):
        """This actually runs the qvality program from PATH."""
        outfn = self.create_outfilepath(self.fn, self.outsuffix)
        command = ['qvality']
        command.extend(self.qvalityoptions)
        command.extend([self.scores['target']['fn'], self.scores['decoy']['fn'],
                        '-o', outfn])
        subprocess.call(command)