Open nick-youngblut opened 1 year ago
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.
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.
The
assert
statement in the code below (and similar assert statements throughout the codebase) do not provide helpful error messages.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 thelocate_genomes()
function). Given the strong possibility for user error, in regards to the input formatting forGT_Pro build
, it would be helpful to include more instructive error messages to help the user understand what is expected.