Python 3.8 global variable not defined

[Travis Lawrence]

When I attempted to run Broccoli with Python 3.8 I got this error:

Traceback (most recent call last): File "broccoli.py", line 145, in <module> broccoli_step1.step1_kmer_clustering(directory, extension, length_kmer, min_aa, nb_threads) File "/Users/5tl/Downloads/Broccoli-1.2/scripts/broccoli_step1.py", line 55, in step1_kmer_clustering results_2 = tmp_res.get() File "/Users/5tl/anaconda3/envs/broccoli/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value NameError: name 'list_files' is not defined

It appears the below hack was broken between Python 3.6 and 3.8:

# convert the parameters to global variables (horrible hack)

I was able to fix this for the first step by zipping together all of the arguments for the process_file function:

files_start = zip(list_files, list_start, list(range(len(list_files))), itertools.repeat(directory), 
                  itertools.repeat(length_kmer), itertools.repeat(min_aa), itertools.repeat(out_dir))

converting the multiprocessing call from map_async to starmap_async:

tmp_res = pool.starmap_async(process_file, files_start, chunksize=1)

and updating the definition for the process_file function and variable assignments to reflect the new starmap_async call:

def process_file(filename, counter, index, directory, length_kmer, min_aa, out_dir):
    ## get back info
    #index = list_files.index(filename)
    #counter = list_start[index]

It seems a similar fix is required for each step of the pipeline to make it compatible with the latest version of Python.

[Romain Derelle]

Thanks for pointing this issue.
I've only used Python 3.6 and wasn't aware of this bug. I will change the readme file to point to Python 3.6 / 3.7 (instead of 3.6+) and will correct the code when I have some time to do it.

[Travis Lawrence]

I can always submit a pull request with the fixes sometime next week if that would work for you.