Example #1
0
    def process_file(self, sequence_file):
        """Processes the given sequence file"""
        self.log.info("Processing file: %s..." % sequence_file)
        sequence_file = os.path.abspath(sequence_file)

        with temporary_dir(change=True) as dirname:
            self.log.debug("Using temporary directory: %s" % dirname)
            ok = self.run_formatdb(sequence_file)
            ok = ok and self.run_blastall(sequence_file)
            if not ok:
                return False

        return True
Example #2
0
    def process_file(self, sequence_file):
        """Processes the given sequence file"""
        self.log.info("Processing file: %s..." % sequence_file)
        sequence_file = os.path.abspath(sequence_file)

        with temporary_dir(change=True) as dirname:
            self.log.debug("Using temporary directory: %s" % dirname)
            ok = self.run_formatdb(sequence_file)
            ok = ok and self.run_blastall(sequence_file)
            if not ok:
                return False

        return True
Example #3
0
    def process_file(self, sequence_file):
        """Processes the given sequence file"""
        self.log.info("Processing file: %s..." % sequence_file)
        sequence_file = os.path.abspath(sequence_file)
        tmp_dir = self.options.temporary_dir

        if tmp_dir is not None:
            tmp_dir = os.path.abspath(tmp_dir)

        if tmp_dir and not os.path.exists(tmp_dir):
            os.makedirs(tmp_dir)

        with temporary_dir(change=True, dir=tmp_dir) as dirname:
            self.log.debug("Using temporary directory: %s" % dirname)
            ok = self.run_formatdb(sequence_file)
            ok = ok and self.run_blastall(sequence_file)
            if not ok:
                return False

        return True