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NetMHCIIpan v3.0 has several differences in its interface that require a separate class and output parser:
- no "-list" command
- no tmp directory option
- warnings with length = 20
- multiple tables …
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From Kipp Akers:
> So I tried in vain to add a bit of code to topiary so that it would take NetMHCIIpan as an input/prediction method, but it keeps dying with the message that one of the arguments m…
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Hey guys, Alex asked me to run the mouse tumors through topiary to generated MHC-II predictions, but I'm having some difficulty running topiary w/ these settings. I've tried a bunch of different input…
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It looks like topiary is losing all but one allele's epitopes when we I run with mhciipan:
```
topiary --mhc-predictor netmhciipan --mhc-alleles DRB1*15:01,DRB1*07:01 --maf /sc/orga/projects/PBG/TCGA…