[Documentation]: Incorrect conversion of nomenclature version 1 allele names to version 3 allele names in USAFEL-UchiTelle-small.pop

[sjmack]

Is your issue related to the main website?

Yes

Is your issue related to documentation?

Yes

Is your issue related to other parts of the documentation?

No

Is your documentation issue...?

both reporting an error and a making a proposed improvement

Describe documentation issue

The allele names in the USAFEL-UchiTelle-small.pop example HLA dataset have been incorrectly updated from their nomenclature version 1 names to nomenclature version 3 names.

For example, the A*03012 allele was converted to A*03:012, but should have been converted to A*03:01:02. There is no A*03:012 allele.

In addition, the Cw*02025 allele was converted to C*02:025, but this allele has been renamed as C*02:10:06. There is no C*02:025 allele.

Manual modification of HLA allele names should not be performed without first consulting the IPD-IMGT/HLA Database or the ANHIG/IMGT-HLA GitHub Repository.

Additional context

No response

[alexlancaster]

@sjmack thanks for the report! Can you also check the listings in the User Guide: http://pypop.org/docs/guide-chapter-usage.html#sample-files

I think some of those files (Listings 2.1-2.3 specifically) might also need updating and potentially also here: http://pypop.org/docs/guide-chapter-instructions.html

[sjmack]

Yes. Listings 2.1, 2.2 and 2.3 in the User Guide also need to be updated.

The alleles in the instructions all seem to be correctly formed. Some of them are truncated versions of longer allele names, but that is not an issue.

[alexlancaster]

@sjmack I updated the specific alleles you mentioned in

https://github.com/alexlancaster/pypop/blob/248-documentation-incorrect-conversion-of-nomenclature-version-1-allele-names-to-version-3-allele-names-in-usafel-uchitelle-smallpop/tests/data/USAFEL-UchiTelle-small.pop

and also the "gold output" for the unit tests.

I also updated those alleles in the docs, see the preview version here:

https://alexlancaster.github.io/beta.pypop.org/docs/guide-chapter-usage.html#sample-files

So an allele like 01:01, is "truncated", i.e. not the most specific allele (i.e. doesn't appear as a separate line in the MSF files), but still valid per se?

Other than the two specific allele changes, are there additional alleles that remain in the docs (.pop file) that still need converting? can you enumerate any additional corrections?

[sjmack]

The updated allele names are accurate now. I do note that B*35:09:01 is a truncated version of 35:09:01:01, but the truncation is okay for analysis in PyPop. Thanks!

[alexlancaster]

The updated allele names are accurate now. I do note that B*35:09:01 is a truncated version of 35:09:01:01, but the truncation is okay for analysis in PyPop. Thanks!

Excellent. Could you review the changes in the PR #251 and approve? then I'll merge with main.