DartModules.py 文件源码

def _run_cdhit(self, fasta_path, identity=0.95, word_size=5, description_length=0, cdhit_path=None):

        """ Run CDHIT-EST for sequences, install with sudo apt install cd-hit on Ubuntu """

        self.messages.get_cdhit_message(identity)

        if cdhit_path is None:
            cdhit_path = "cd-hit-est"

        file_name = self.project + "_IdentityClusters_" + str(identity)

        out_file = os.path.join(self.tmp_path, file_name)
        cluster_path = os.path.join(self.tmp_path, file_name + '.clstr')

        with open(os.devnull, "w") as devnull:
            call([cdhit_path, "-i", fasta_path, "-o", out_file, "-c", str(identity), "-n", str(word_size),
                  "-d", str(description_length)], stdout=devnull)

        return cluster_path