[이왜안?] AttABseq code error

 

• 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.
• On line 10 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 crossvalid/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).
• 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