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shannon's Issues

remove duplicated code - calling run_MB_SF_fn.py

In shannon.py this code is duplicated:

if main_server_parameter_string and inDisk:
    if run_parallel and nJobs > 1:
        cmds = []
        for param_str in main_server_parameter_string.split():
            cmds.append(python_path + " " + shannon_dir + "run_MB_SF_fn.py " + param_str + " --run_alg " + mb_sf_param_string + " --kmer_size " + str(K) + " " +
                        paired_end_flag + " --dir_name " + comp_directory_name + " " + param_str + " --shannon_dir " + shannon_dir + " --python_path " + python_path)
        cmds = tuple(cmds)
        run_parallel_cmds.run_cmds(cmds, nJobs)
    else:
        for param_str in main_server_parameter_string.split():
            run_cmd(python_path + " " + shannon_dir + "run_MB_SF_fn.py " + param_str + " --run_alg " + mb_sf_param_string + " --kmer_size " + str(K) + " " +
                    paired_end_flag + " --dir_name " + comp_directory_name + " " + param_str + " --shannon_dir " + shannon_dir + " --python_path " + python_path)

build the command string once, outside the if/else. only tupelize and call run_cmd() vs run_parallel_cmds.run_cmds in the if/else as it's clearer

remove code duplication - run_MB_SF_fn.py

In shannon.py, there's duplicate code that builds the run_MB_SF_fn.py command line:

if main_server_parameter_string and inDisk:
    if run_parallel and nJobs > 1:
        cmds = []
        for param_str in main_server_parameter_string.split():
            cmds.append(python_path + " " + shannon_dir + "run_MB_SF_fn.py " + param_str + " --run_alg " + mb_sf_param_string + " --kmer_size " + str(K) + " " +
                        paired_end_flag + " --dir_name " + comp_directory_name + " " + param_str + " --shannon_dir " + shannon_dir + " --python_path " + python_path)
        cmds = tuple(cmds)
        run_parallel_cmds.run_cmds(cmds, nJobs)
    else:
        for param_str in main_server_parameter_string.split():
            run_cmd(python_path + " " + shannon_dir + "run_MB_SF_fn.py " + param_str + " --run_alg " + mb_sf_param_string + " --kmer_size " + str(K) + " " +
                    paired_end_flag + " --dir_name " + comp_directory_name + " " + param_str + " --shannon_dir " + shannon_dir + " --python_path " + python_path)

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