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Order according the peptide order form #2

Closed evelyn-schmidt closed 12 months ago

evelyn-schmidt commented 1 year ago

a slightly annoying problems is that the neoantigen candidates file and the Peptide 51mer are not in the same order, which results in a slight inconvenience when manually reviewing. @malachig and I have discussed making the neoantigen candidates sheet in the same order as the peptides 51mer sheet.

I think this will have to happen in the setup_review script so that when those sheets are read in by the color_peptides51mer they are already in the correct order. color_peptides51mer uses a universe ID so maybe that step can be moved into the setup_review script.

https://github.com/griffithlab/neoag_vaccine_scripts/blob/7de6ef1c074b83af12a146f724e9780f4f322410/scripts/color_peptides51mer.py#L252-L259

evelyn-schmidt commented 12 months ago

A new id was created to sort the neoantigen review in the same order as the peptide order form. The id uses gene and transcript since that is the only information that both sheets have that assure that they will be always in the same order.

https://github.com/griffithlab/neoag_vaccine_scripts/blob/1514326d1f42a610212c93c9fb9397b2c9d59635/scripts/generate_reviews_files.py#L87-L88

https://github.com/griffithlab/neoag_vaccine_scripts/blob/1514326d1f42a610212c93c9fb9397b2c9d59635/scripts/generate_reviews_files.py#L107-L115