ea7f042c7a0a9ca1bef59bf06c4f48da6aca931a,chiron/utils/file_batch.py,,extract,#,24

Before Change

            return True
        return False

    for file_n in os.listdir(root_folder):
        if file_n.endswith("fast5"):
            if output_file is None:
                output_file = open(output_folder + os.path.sep + "data_batch_" + str(batch_idx) + ".bin", "wb+")

After Change

            return True
        return False

    for base_dir, _ ,file_list in os.walk(root_folder):
     for file_n in file_list:
        if file_n.endswith("fast5"):
            if output_file is None:
                output_file = open(os.path.join(output_folder,"data_batch_" + str(batch_idx) + ".bin"), "wb+")
            output_state = extract_fast5(os.path.join(base_dir,file_n), output_file)
            if output_state:
                batch_idx += 1
                output_file.close()
                if (FLAGS.max is not None) and (batch_idx > FLAGS.max):
                    sys.stdout.write("Reach the maximum %d batch number, finish read." % (FLAGS.max))
                    break
                output_file = open(output_folder + os.path.sep + "data_batch_" + str(batch_idx) + ".bin", "wb+")
                sys.stdout.write("%d batch transferred completed.\n" % (batch_idx - 1))
    sys.stdout.write("File batch transfer completed, %d batches have been processed\n" % (batch_idx - 1))
    sys.stdout.write("%d files scussesfully read, %d files failed.\n" % (len(success_list), len(fail_list)))
    if not output_state:
        output_file.close()

Instances