TLStab is our transfer learning-based pMHC stability predictor.

To use TLStab, you will first need to be under the TLenv environment (see instructions on the top README file on how to install and activate the TLenv conda environment.

An input .csv file that has at least an allele and a peptide column is needed (an example of SARS-CoV-2 peptides can be found in the examples folder).

Given the .csv, TLStab can be used as follows:

 python TLStab.py examples/SARS-CoV-2_peptides_example.csv 

This will result in an output file named TLStab_out.csv with pMHC stability predictors for each peptide-allele pair (in half life minutes) in the 3rd column.

Finally, to specify a specific output file name, one can use something like the following:

 python TLStab.py examples/SARS-CoV-2_peptides_example.csv --out Desired_output_filename.csv