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X-lab-3D / PANDORA

MODELLER-based, anchor restrained, Peptide-MHC Modelling pipeline
Apache License 2.0
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allele type must be a list #162

Closed v-mikhaylov closed 1 year ago

v-mikhaylov commented 2 years ago

The first example in the tutorial suggests to use target = PMHC.Target(id = 'myTestCase' allele_type = 'HLA-A*0201' peptide = 'LLFGYPVYV', anchors = [2,9]) However, I notice that when I use a string as an argument in allele_type, PANDORA often assigns templates with non-matching MHC even for HLA-A02:01. If I replace that line by `allele_type = ['HLA-A0201']`, it assigns templates correctly. Does allele_type have to be a list?

DarioMarzella commented 2 years ago

Hi @v-mikhaylov , thanks for opening this issue. This is indeed a problem of the README. The current release of PANDORA needs the allele to be a list (as explained here ). I will fix the README asap. Also, we are working on the next release of PANDORA, which should be able to use either a list or a string.

DarioMarzella commented 2 years ago

Tutorial fixed in b9ef5f1

v-mikhaylov commented 2 years ago

Thanks! It is a little dangerous that the algorithm doesn't throw an error when provided with a string, since this is what many users may naturally do even if it is not recommended by the manual, and some result will be produced, so they won't notice the problem. If I may suggest, you might want to add an assertion that checks the type.

DarioMarzella commented 2 years ago

Absolutely agree with you. This will not be a problem for the new release, but I should add an assertion with a hotfix to the current master repo.

DarioMarzella commented 1 year ago

As a new release is coming soon (now in pre-release v2.0.0-alpha) including these changes, this will most likely not be fixed in the main.