-
Notifications
You must be signed in to change notification settings - Fork 87
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
QC for Chlamydomonas reinhardtii #890
Comments
Hi @aays, thanks for contributing to stdpopsim. I will be QCing your species. Do you have an update on the publication of the raw recombination data? |
I will create the PR once I get the raw recombination map.
|
Hi @izabelcavassim, thanks for the QC! I did indeed upload the raw recombination data to figshare in #950 (the specific link can be found here). Please let me know if anything else is missing! |
Great @aays I will be looking at the figshare files and updating the values in the test scripts! Will let you know once I am done so you can have a look at that PR! Thanks! |
@aays - in #1067 @izabelcavassim wondered where the generation time estimate came from, but maybe you missed it? |
Thanks for the heads up @petrelharp - I've added an explanation on the PR! |
can you close this @petrelharp? sorry forgot to mention in my other PR |
Yes! And gee you should be able to also. I've sent you an invite that should get you those permissions... |
PR for new species: #863
IMPLEMENTER'S NOTE: The recombination rates are from Hasan and Ness 2020, but the raw values were not published as part of the manuscript - per @jeromekelleher's advice I'll be uploading them to figshare and updating the doi.
The per-chromosome mutation rates will also hopefully be added in as a separate PR (I was just sent the data late yesterday) and I'll be asking about whether I can make those public as well - though it's not my data, so TBD!
If you volunteer to QC this species, please use the checklist below.
While this list is intended to be comprehensive, it may not be exhaustive.
Where relevant, the QC reviewer should identify that parameter values match
those given in the linked citation(s).
The QC reviewer should start a pull request that fills out the test stubs
with independently obtained values. The reviewer may look at the python code
for rationale provided in comments, but should ignore the actual code
as much as possible - comments in the code should give enough information
that it's obvious how to get the correct value from the provided references.
(In particular, we shouldn't copy-paste the value from the code into the test!)
For each citation, check:
Citations are required for:
The final PR should:
pytest.mark.skip
lines that make the tests not runThe text was updated successfully, but these errors were encountered: