Map out tempo output files to NeoantigenEditing input

[nikhil]

Of the 4 indicated input files:

iedb.fasta

a resource

epitope_distance_model_parameters.json

a resource created by the lab https://github.com/LukszaLab/NeoantigenEditing/blob/0126b82b1b4c0d44b6e3f5559c43e6022b8cdbd3/data/epitope_distance_model_parameters.json

fitness_weights.txt

no idea what this is https://github.com/LukszaLab/NeoantigenEditing/blob/0126b82b1b4c0d44b6e3f5559c43e6022b8cdbd3/data/fitness_weights.txt

patient_data

Mutation data under a clonal tree https://github.com/LukszaLab/NeoantigenEditing/blob/0126b82b1b4c0d44b6e3f5559c43e6022b8cdbd3/data/Patient_data/11-LTS/Primary/11_LTS_primary_tumor.json

After reading the methods of the paper it looks like you need: HLA typing, they use OptiType Clones created by PhyloWGS NetMHC?

Basically, we first need to know what information to gather to form the input files, and then we can focus on formatting it properly

[nikhil]

looks like we will run only 1 and 2, might need to fork the code to get the specific calculations we need for step 2

[nikhil]

Example of a fork someone else did: https://github.com/LukszaLab/NeoantigenEditing/compare/main...LCR-BCCRC-Steidl-Lab:NeoantigenEditing_fork:main#diff-7849ed4b5e38dcf9ebb66e5159c59181e99a3de20f7ff1f619881c723532c5bcR329

[nikhil]

It looks like the input of this file: https://github.com/LukszaLab/NeoantigenEditing/blob/main/data/Patient_data/11-LTS/Primary/11_LTS_primary_tumor.json, is just the phylowgs + OptiType

[johnoooh]

I'll work on this as well

[nikhil]

https://docs.google.com/document/d/1gj4UgrihULmM5DyrzT8yAJty3W5gGHAuxfiQeoq8YPo/edit?usp=sharing