`assert os.path.isdir(in_dir)` => no helpful error message

[nick-youngblut]

The assert statement in the code below (and similar assert statements throughout the codebase) do not provide helpful error messages.

def locate_genomes(in_dir):
    assert os.path.isdir(in_dir) 
    fpaths = []
    for f in os.listdir(in_dir):
        fpath = in_dir.rstrip('/')+'/'+f
        if os.path.isfile(fpath) and fpath[-4:] == ".fna" or fpath[-3:] == ".fa":
            fpaths.append(fpath)
            sys.stderr.write("\tgenome path found: {}\n".format(fpath))

    sys.stderr.write("{} genomes sequences will be used for database building\n".format(len(fpaths)))

    return fpaths

While https://www.sciencedirect.com/science/article/pii/S2666166722008449 is nice to have, I am still trying to figure out the correct input directory structure and file naming for GT_Pro build (e.g., reference genome fasta files must end in *.fna or .fa according to the locate_genomes() function). Given the strong possibility for user error, in regards to the input formatting for GT_Pro build, it would be helpful to include more instructive error messages to help the user understand what is expected.

[nick-youngblut]

In regards to input formatting, it would be helpful to clearly point out in the instructions that compressed genome fasta files are not allowed as input for either maast or GT_Pro build... or just allow for at least gzip'ed input fasta files.

[nick-youngblut]

Another example where the assertion error is not very helpful:

Traceback (most recent call last):
  File "/opt/gt-pro/scripts/build_db.py", line 402, in <module>
    main()
  File "/opt/gt-pro/scripts/build_db.py", line 388, in main
    path_objs = validate_input_paths(input_array)
  File "/opt/gt-pro/scripts/build_db.py", line 112, in validate_input_paths
    assert os.path.isfile(path_map['species_dir'] + vtarget)
AssertionError

It would be helpful to include something like Could not find 'msa.fna'. Why must the tag_msa.fa generated from MAAST be renamed as msa.fna? Both the basename & extension must be renamed.