The default length do not work wit NetMHCpanII

griffithlab / pVACtools

http://www.pvactools.org

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The default length do not work wit NetMHCpanII #539

Closed riederd closed 4 years ago

riederd commented 4 years ago

https://github.com/griffithlab/pVACtools/blob/e6fbd8dccdbd2de4042d2d413c30aebbc7f8995d/lib/run_argument_parser.py#L48

see pVACtools docker /opt/iedb/mhc_ii/mhc_II_binding.py line 246 The minimum length is 15.

riederd commented 4 years ago

...furthermore mhc_II_binding.py is not using the provided lengths at all, it always uses 15. sys.argv[4] is not parsed by that script, so netMHCIIpan is run with the default length of 15. See NetMHCIIpan-3.1.pl line 134.

riederd commented 4 years ago

....and mhcii_predictor.py from IEDB tools imported by mhc_II_binding.py is only working with length 15.

susannasiebert commented 4 years ago

Can you please check which version of the IEDB class II package you are on? I ran into this problem with an older version of the IEDB package we are using in our current Docker containers. Since this is a new feature from IEDB it doesn't work with older IEDB versions. I had to upgrade to class II package to version 2.22.3 to get this new feature.

susannasiebert commented 4 years ago

I will also confirm on my end whether this feature works for NetMHCpanII specifically in the 2.22.3 package.

susannasiebert commented 4 years ago

I confirmed that in a container with IEDB class ii 2.22.3 predictions with different epitope lengths for NetMHCpanII work as expected. My test command was:

pvacbind download_example_data .
source activate pvactools_py27
python mhc_ii/mhc_II_binding.py NetMHCIIpan HLA-DRB1*03:01 pvacbind_example_data/input.fasta 12

I used the susannakiwala/pvactools:2.0.0-alpha.2 container

riederd commented 4 years ago

I'm on 2.17.6 downloaded from https://downloads.iedb.org/tools/mhcii/2.17.6/IEDB_MHC_II-2.17.6.tar.gz as indicated in your docker file from https://github.com/griffithlab/docker-pvactools/blob/master/Dockerfile

susannasiebert commented 4 years ago

yes, the 2.17.6 version of IEDB class II unfortunately does not have the epitope length feature. You will need to either make a new docker container that has the newest IEDB class II version or you are welcome to try out susannakiwala/pvactools:2.0.0-alpha.2 which has that version installed. It also already has to correct version of the pVACtools code.

riederd commented 4 years ago

Oh, great. I'm using a slightly extended image that also includes the tools to do readcount annotations and so on, so I have to rebuild it anyway.

riederd commented 4 years ago

I just rebuild my singularity image and I can confirm it works nicely with the ISDB version 2.22.3 Thanks

susannasiebert commented 4 years ago

Wonderful. I assume we can close this issue then?

riederd commented 4 years ago

sure, thanks again