search

alexlancaster / pypop

PyPop: Python for Population Genomics
http://pypop.org
GNU General Public License v2.0
22 stars 15 forks source link

update the links in docs on allele names #137

Closed alexlancaster closed 10 months ago

alexlancaster commented 11 months ago

There's a section in the docs about the different allele names used for creating the CustomBinning rules:

The Anthony Nolan list of deleted allele names (http://www.anthonynolan.com/HIG/lists/delnames.html); and the Ambiguous Allele Combinations, release 2.18.0 (http://www.ebi.ac.uk/imgt/hla/ambig.html).

(see http://pypop.org/docs/guide-chapter-usage.html#id8)

but all the links are 404. @rsingle can you supply the updated versions / new links for these references?

rsingle commented 11 months ago

Yes. We should probably download new versions of the files too.

alexlancaster commented 11 months ago

Yes. We should probably download new versions of the files too.

agree. but I wonder in the meantime, if we could at least provide some updated links? I don't want the 1.0.0 release to be contingent on getting every last thing updated, since we can make new minor releases to fix them (e.g. in 1.0.1 or later).

alexlancaster commented 10 months ago

@rsingle Also I noticed that we say just above the links:

PyPop is distributed with a biologically relevant set of CustomBinning rules that have been compiled from several sources

But the only place I can find in the repo where we compile a comprehensive list of such rules is in this file, is this what is meant?

https://github.com/alexlancaster/pypop/blob/65788c6d1f37708be768a92d6509b8425c82c4f2/website/html_root/popdata/2008/config-allelecount.ini#L82-L213