Add pyrho genetic maps #572
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-Added genetic maps for the 26 populations from Phase 3 of the 1000 Genomes Project that were inferred using pyrho for Spence and Song 2019. -Alphabetized citations.
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thanks for the PR @jeffspence. it looks like one thing that is breaking the tests currently is the URL-- would you mind putting this on a publicly accessible address for a minute so that the PR can pass tests? @ndukler do we have a SOP on how to deal with map downloading / caching before we merge? |
| file_pattern=( | ||
| "Pyrho{}_GRCh37_chr{{id}}.txt".format(pop)), | ||
| citations=[ | ||
| stdpopsim.Citation( |
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maybe pull this citation out of here and set it to _spence_song_2019 as with the other citations?
I haven't actually uploaded the maps yet so I expect the tests to fail. I just asked @jeffspence to throw up the PR so I could take a look through and make sure everything was in order. It looks pretty good so I'll upload the maps now. |
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it would be great to have a sandbox to stage these things in during development. at the start we were just hosting them locally on various servers, but since we moved to AWS it's a bit harder |
I agree, but it's fairly easy to just throw things up on AWS, even this only took a half hour or so and this was absolutely massive by our standards. In fact, we can only do something of this size twice more before we run out of our 2GB allowance :). Which is really my way of saying nice work @jeffspence , this is an awesome resource for us to have. Anyway, it's all up now so I just re triggered the travis build so lets see if it works. |
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Just as a record, I think I was wrong, the files do have to be flat in the |
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Ok, so things look good! I cannot trigger a manual rebuild for CircleCI or appveyor so add a comment somewhere, rebase and force push to get it going again @jeffspence . |
Codecov Report
@@ Coverage Diff @@
## master #572 +/- ##
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Coverage 99.64% 99.65%
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Files 29 29
Lines 1997 2000 +3
Branches 206 207 +1
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+ Hits 1990 1993 +3
Misses 3 3
Partials 4 4
Continue to review full report at Codecov.
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Thanks @ndukler and @andrewkern ! It was a real pleasure! |
I added genetic maps for Homo sapiens for the 26 populations in Phase 3 of the 1000 Genomes Project from my paper here: https://advances.sciencemag.org/content/5/10/eaaw9206
I also alphabetized the references at the top of
stdpopsim/catalog/HomSap/__init__.pyI'd be happy to make any additional changes (e.g., are genetic maps unit tested?).