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griffithlab / neoag_vaccine_scripts

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Generate both sheets with all candidates not just the ones marked accepted/reviewed #19

Open evelyn-schmidt opened 6 months ago

evelyn-schmidt commented 6 months ago

Just had to generate a 51mer sheet will all sequences colored. I had to comment out these lines to allow for all candidates despite their review status to be included in the final review files:

https://github.com/griffithlab/neoag_vaccine_scripts/blob/8c5d9a110bb9102d55bdcc600d36849bde8ff777/scripts/generate_reviews_files.py#L108-L109

Also change these two lines to make sure that the sequences are colored despite the classI and classII alleles not passing our thresholds. https://github.com/griffithlab/neoag_vaccine_scripts/blob/8c5d9a110bb9102d55bdcc600d36849bde8ff777/scripts/color_peptides51mer.py#L85

https://github.com/griffithlab/neoag_vaccine_scripts/blob/8c5d9a110bb9102d55bdcc600d36849bde8ff777/scripts/color_peptides51mer.py#L109

These two things should probably be able to be turned on and off as the user wants them -- or the thresholds be able to be set in the run command