buildhmm.py 文件源码

def __init__(self, query, target_id, database, tk_root, tk_config, pseudo=True, ss=True, cpu=1):

        self.tk_root = tk_root
        self.tk_config = tk_config
        self.hhlib = os.path.join(tk_root, "bioprogs", "hhsuite")

        if 'TK_ROOT' not in os.environ or not os.environ['TK_ROOT']:
            os.putenv('TK_ROOT', self.tk_root)
        if 'HHLIB' not in os.environ or not os.environ['HHLIB']:
            os.putenv('HHLIB', self.hhlib)
        os.environ["PATH"] += os.pathsep + os.path.join(self.hhlib, "bin")

        self.query = query
        self.accession = target_id[:-1]
        self.chain = target_id[-1]
        self.database = database
        self.pseudo = bool(pseudo)
        self.ss = bool(ss)
        self.cpu = cpu

        self._input = None
        self._a3m = None
        self._hhm = None

        self.configure_input()