Some code Errors in AttABseq

[DBpackage]

1. Instead of running the main.py executable file located in the root of the AttAbSeq GitHub repository,
   you must run the main_AB___.py file located in the crossvalid/script/ directory.

2. On line 10 (or around) of the script, the import statement from model import * must be changed.
   It should be modified to import from the corresponding model_AB___.py file, which is also located inside the cross_validation/script/ directory. The specific model file should match the main script you are running (e.g., if running main_AB001.py, you should import from model_AB001.py).

3. The existing Swiss-Prot database provided with the git clone is an incomplete file and is not suitable for running the main script. Therefore, you must delete all the Swiss-Prot DB files from the following path and download a new, complete version.

Path to the files that need to be deleted: AttABseq/cross_validation/ncbi-blast-2.12.0+/bin/
Files to delete: swissprot*, taxdb.bti

Next, set the execution permission for the update_blastdb.pl script using chmod.
Then, use the following commands to download the complete Swiss-Prot database files.
This is necessary for the code that retrieves PSSMs from the main script to run correctly.

Navigate to the BLAST bin directory

cd YOURPATHTO/AttABseq/cross_validation/ncbi-blast-2.12.0+/bin/

Set execution permission for the update script (if needed)

chmod +x update_blastdb.pl

Run the script to download the complete Swiss-Prot database

./update_blastdb.pl --decompress swissprot

I hope that these information helps users