Python Session.refresh方法代碼示例

# 需要導入模塊: from hpf.hddb.db import Session [as 別名]
# 或者: from hpf.hddb.db.Session import refresh [as 別名]

#.........這裏部分代碼省略.........
        """Variables:
        self.prediction - The PsipredPrediction object returned from Psipred32(...).run()
        self.dbo        - If dbstore=True, the Psipred ORM object (DataBaseObject) from the HPF DB
        """
        from hpf.hddb.db import Session, Sequence

        self.sequence_key  = sequence_key
        self.nr_db = os.path.abspath(os.path.expanduser(nr_db))
        self.ginzu_version = ginzu_version
        self.dir = dir if dir else os.getcwd()
        self.dbstore = dbstore
        self.debug = debug

	#kdrew: commenting out because "nr" is not a file but a location
        #if not os.path.isfile(self.nr_db):
        #    raise Exception("Must provide a valid NR database file")
        
        self.session  = Session()
        self.sequence = self.session.query(Sequence).get(self.sequence_key)
        if not self.sequence:
            raise Exception("No sequence with key {0} exists in DB".format(self.sequence_key))
        
        self.fasta_file = "{0}.fasta".format(self.sequence_key)
        self.chkpt_file = "{0}.chk".format(self.sequence_key)
        self.psipred_file = "{0}.psipred".format(self.sequence_key)

        # Set in run (dbo optionally)
        self.prediction = None
        self.dbo = None

        if autorun:
            self.prediction = self.run()

    def get_prediction_string(self, ):
        """Returns the prediction string from the PsipredPrediction object (if populated)"""
        if not self.prediction:
            return None
        return self.prediction.prediction

    def run(self, ):
        """
        Cobbles together elements for running Psipred (writes fasta, runs blast to get checkpoint,
        runs psipred and psipass2, and then parses results and uploads to DB if set to).
        IF dbstore is true, adds Psipred ORM object to hpf database and sets self.dbo.
        RETURNS hpf.pdb.psipred.PsipredPrediction object
        """
        import subprocess
        from Bio import SeqIO
        from Bio.Blast.NCBIStandalone import blastpgp
        from hpf.hddb.db import Psipred as PsipredORM, PsipredFactory
        from sqlalchemy.exc import IntegrityError

        # Write fasta file
        if self.debug: print "Psipred: writing fasta file"
        with open(self.fasta_file, 'w') as handle:
            SeqIO.write([self.sequence.record], handle, "fasta")

        # Get exe path and run blast
        if self.debug: print "Psipred: running blastpgp against '{0}' DB to create checkpoint file".format(self.nr_db)
        blast_cmd = subprocess.Popen(["which", "blastpgp"], stdout=subprocess.PIPE).communicate()[0].strip()
        result,error = blastpgp(blastcmd=blast_cmd, 
                                program='blastpgp', 
                                database=self.nr_db, 
                                infile=self.fasta_file, 
                                npasses=3, 
                                checkpoint_outfile=self.chkpt_file, 
                                expectation=1e-4, 
                                model_threshold=1e-4, 
                                align_outfile="/dev/null")
        # Note: must call something that blocks on blastpgp results (need to wait for cmd to finish)
        res = result.read()
        err = error.read()
        if self.debug:
            print "Result: ", res
            print "Error/Warning: ", err

        # Create Psipred options object and run Psipred 3.2 on them
        if self.debug: print "Psipred: running Psipred 3.2"
        options = PsipredOptions(self.fasta_file,
                                 profile=self.chkpt_file,
                                 output=self.psipred_file+".1",
                                 output2=self.psipred_file+".2",
                                 horiz=self.psipred_file,
                                 cwd=self.dir)
        self.prediction = Psipred32(options).run()
        
        # Add to database (optional) and return
        if self.dbstore:
            if self.debug: print "Psipred: adding psipred DBO to hpf database"
            psipred_dbo = PsipredFactory().create(self.prediction, sequence_key=self.sequence.id, ginzu_version=self.ginzu_version)
            self.session.add(psipred_dbo)
            try:
                self.session.commit()
            except IntegrityError:
                print "Psipred entry for <seq {0}, ginzu_version {1}> already exists in DB. Returning existing object".format(self.sequence_key, self.ginzu_version)
                self.session.rollback()
                psipred_dbo = self.session.query(PsipredORM).filter_by(sequence_key=self.sequence.id, ginzu_version=self.ginzu_version).first()
            self.session.refresh(psipred_dbo)
            self.dbo = psipred_dbo
        return self.prediction