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Processing Peptide Lists
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Created by: Elizabeth Borden
Last updated: 12/10/2020
Purpose: This pipeline is designed to take a list of peptides and generate a list of prioritiation terms for each one that can then be used with my logistic regression model to get a prioritized list of peptides. 

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Input files
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Directory structure
Dataset directory
    Validated_All.txt
    /HLAA2.1
        HLAA2.1_peptides.in

HLAA2.1_peptides.in contains peptide list in the format:
>Peptide
Peptide
>Peptide
Peptide
etc. 

Validated_Al.txt contains the validation results. Most of the formatting does not matter but column 2 needs to be the HLA type and column 5 needs to be the peptide and column 9 needs to be the validation results. If these columns are changed, just need to edit the column numbers in Prep_final_file.R and Prep_luksza_input.R.

Config file should be in the following format with a line for each HLA type
"all_samples": [
"HLAA2.1"
],


"HLAA2.1":{
"hla": ["HLA-A02:01"]
}
}

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Steps
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Run start_processing_peptides-snakemake.py
Run join.sh (Note there is a lot of hard coded content in this one right now, so editing required)
Run start_processing_peptides_part2-snakemake.py