raghavagps/HAIRpred ? reverse-engineered prompt

Build me a Python command line tool that predicts human antibody interacting residues in a protein or peptide sequence from a FASTA file or one sequence per line.

I want it to take an input file, write results to a CSV file, and let me choose between a prediction mode and a design mode. For prediction, support two model choices, one using RSA only and one using RSA plus PSSM, with the second one as the better default. Let me also set a threshold from 0 to 1, with 0.5 as the default.

Please make it work as a standalone script I can run from the terminal, and include clear help text for the arguments. If the models or feature files need to be loaded from the repo, wire that up too. Use the existing dataset and model files in the project, and if you need to check current setup details for DSSP or PSI BLAST, look up the latest docs online. I’d like it to feel ready to run on Linux with minimal extra steps.