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griffithlab / neoag_vaccine_scripts

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Best Transcript can be different #1

Closed evelyn-schmidt closed 12 months ago

evelyn-schmidt commented 1 year ago

https://github.com/griffithlab/neoag_vaccine_scripts/blob/7de6ef1c074b83af12a146f724e9780f4f322410/scripts/color_peptides51mer.py#L302-L304

When the best transcript is different for the classI peptide and the classII peptide, neither are highlighted. I believe that this ID contains the best transcript which is used in searching the classI and classII pvac aggregated report. Maybe I will have to change how this ID looks or used something other than transcriptID to identify classI and classII peptides.

evelyn-schmidt commented 12 months ago

The classI and classII sequence are gathered into one dataframe before joining with the 51mer. The join ID only contains the classI transcript so attaching the classII sequence to the classI first allows for both sequences to then be joined with the 51mer.

https://github.com/griffithlab/neoag_vaccine_scripts/blob/1514326d1f42a610212c93c9fb9397b2c9d59635/scripts/color_peptides51mer.py#L238-L268