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griffithlab / pVACtools

http://www.pvactools.org
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Add support for dog alleles for NetMHCpan #1131

Open susannasiebert opened 3 months ago

susannasiebert commented 3 months ago

When running the IEDB MHC I tool via the API, there are three dog alleles supported for NetMHCpan (ba and el): DLA-8803401, DLA-8850101, DLA-8850801. These alleles are not enabled in the IEDB MHC I standalone software (version 3.1.5). A request has been submitted with IEDB to have these alleles be enabled in the standalone tool. Once that is completed, we can add these alleles to our internal list to enable them in pVACtools. This also requires updating the Docker container to use the IEDB version supporting these alleles.

susannasiebert commented 3 months ago

IEDB MHC I 3.1.6 has been released and supposedly adds support for these alleles to NetMHCpan. However, after installing and testing this version locally I have been unable to get them to work. 

$ ./src/predict_binding.py netmhcpan_ba DLA-8803401 9 ./examples/input_sequence.fasta
2024-08-14:10:29:18,662 WARNING  [__init__.py:662] did not find allele distance info from netmhcpan_output
'NoneType' object is not iterable

Additionally, when running ./src/predict_binding.py netmhcpan_ba mhc | grep DLA I don't get any results.

I have filed a followup issue with IEDB and am awaiting their reponse.