species QC to ChlRei #1067

izabelcavassim · 2021-10-27T19:07:18Z

QC for Chlamydomonas reinhardtii #890, #863, #950

fill out the test stubs
delete the pytest.mark.skip lines that make the tests not run
make sure they pass, talking to the original author to figure out discrepancies

@aays Can you explain where you got your generation time from? For now I don't know the source.
Thanks.

izabelcavassim · 2021-10-27T23:51:51Z

OK, so we are disagreeing on the mutation rate estimates @aays. The Ness 2015 et al, gives me a genome-wide mutation rate that is: 9.63 * 1e-10. Where did you find the per chromosome mutation rate? If not cited then I believe you should also upload it to figshare and change the citation source for the mutation rate (I can do that).

Thank you.

petrelharp · 2021-10-28T06:43:46Z

Where did you find the per chromosome mutation rate? If not cited then I believe you should also upload it to figshare and change the citation source for the mutation rate.

I think that @aays has, at this link, and it's cited already? (ps nice job tracking that down, @aays!)

izabelcavassim · 2021-10-28T16:40:07Z

ah my bad, I think I was reviewing the first version of his PR.

codecov · 2021-10-28T16:52:05Z

Codecov Report

Merging #1067 (52dc0c2) into main (cfd3bf8) will increase coverage by 0.00%.
The diff coverage is n/a.

❗ Current head 52dc0c2 differs from pull request most recent head 5f93436. Consider uploading reports for the commit 5f93436 to get more accurate results

@@           Coverage Diff           @@
##             main    #1067   +/-   ##
=======================================
  Coverage   99.52%   99.52%           
=======================================
  Files          92       91    -1     
  Lines        2934     2941    +7     
  Branches      350      354    +4     
=======================================
+ Hits         2920     2927    +7     
  Misses          6        6           
  Partials        8        8

Impacted Files	Coverage Δ
stdpopsim/catalog/ChlRei/species.py	`100.00% <ø> (ø)`
stdpopsim/__init__.py	`94.73% <0.00%> (-0.27%)`	⬇️
stdpopsim/slim_engine.py	`99.73% <0.00%> (-0.01%)`	⬇️
stdpopsim/genomes.py	`100.00% <0.00%> (ø)`
stdpopsim/catalog/AnaPla/species.py	`100.00% <0.00%> (ø)`
stdpopsim/dfe.py
stdpopsim/models.py	`99.11% <0.00%> (+0.27%)`	⬆️

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izabelcavassim · 2021-10-28T16:53:05Z

OK I think I am done here, @petrelharp you can merge this if you will!

izabelcavassim · 2021-10-28T16:53:50Z

closes #890

petrelharp · 2021-10-28T23:15:14Z

tests/test_ChlRei.py

    def test_qc_population_size(self):
-        assert self.species.population_size == -1
+        assert self.species.population_size == 1.4 * 1e-7

    @pytest.mark.skip("Generation time QC not done yet")


whoops, you've still got a skipped QC test here?

Ah, I see - no reference for this to check yet.

oh wait - I see

stdpopsim.Citation( author="Vitova et al.", year=2011, doi="https://doi.org/10.1007/s00425-011-1427-7", reasons={stdpopsim.CiteReason.GEN_TIME}, ),

hm, but I don't see a natural generation time in that paper on a quick skim anyhow

tests/test_ChlRei.py

petrelharp · 2021-10-28T23:17:39Z

tests/test_ChlRei.py

+        print("This is the mutation rate")
+        print(self.genome.get_chromosome(name).mutation_rate)


Suggested change

print("This is the mutation rate")

print(self.genome.get_chromosome(name).mutation_rate)

whats is the change here? spacing?

Ah, sorry - I was suggesting you delete the print( )s, since they looked like they were just left over from debugging?

izabelcavassim · 2021-10-29T02:32:47Z

I don’t fond it either.

On Thu, 28 Oct 2021 at 16.23, Peter Ralph ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In tests/test_ChlRei.py <#1067 (comment)> : > def test_qc_population_size(self): - assert self.species.population_size == -1 + assert self.species.population_size == 1.4 * 1e-7 @pytest.mark.skip("Generation time QC not done yet") hm, but I don't see a natural generation time in that paper on a quick skim anyhow — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1067 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3WMCL5PHIS6FSIO7L4643UJHLOTANCNFSM5G3CWA7A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Postdoctoral Researcher Dept. of Ecology and Evolutionary biology University of California - Los Angeles (UCLA) - United States Phone: +1 (310) 593-1637 E-mail: ***@***.*** https://izabelcavassim.github.io/ Linkedin profile <https://www.linkedin.com/profile/view?id=350503047&trk=nav_responsive_tab_profile>

izabelcavassim · 2021-10-29T18:05:50Z

OK @aays , I am almost there, I just need to find out where you got the generation time from. Once you do give me the citation I will finish my modifications.

aays · 2021-10-30T16:53:14Z

Very sorry for not getting to this sooner, the past two days were a bit more hectic than I'd have liked! Thanks very much for your comments and review so far @izabelcavassim and @petrelharp.

The generation time was calculated from Vitova et al's estimate of the doubling time at 20 degrees Celsius of 0.10 mitoses / h (p. 604 in the paper, listed as 'doubling / h').

From that, I obtained 876 generations per year (0.10 doublings/h * 24 h * 365 days) hence 1/876 as the generation time. C. reinhardtii can also undergo meiosis, but is expected to have a meiotic cycle once every ~840 generations (e.g. only once a year) based on this work of ours.

This is the best data I know of on C. reinhardtii's generation time, I'm afraid. Please let me know if this sounds reasonable!

petrelharp · 2021-11-01T15:44:29Z

Ok - so it should be clear somewhere that generation time is time between mitotic divisions. And, since mutation rate and recombination rate are in units of "per generation", are those correct here?

izabelcavassim · 2021-11-01T20:36:11Z

also, don't we assume generation time to be in years?

aays · 2021-11-01T21:27:03Z

Ok - so it should be clear somewhere that generation time is time between mitotic divisions. And, since mutation rate and recombination rate are in units of "per generation", are those correct here?

They are! Mutation rate was calculated directly from MA experiments, but the recombination rates listed here are population recombination rates (e.g. Ne * r calculated from genetic diversity) instead of estimates from lab crosses. I elaborated how I dealt with facultative sex a bit further in #863, reproduced here:

An important note re: the recombination rate - sex takes place once every ~840 generations in the species (it's facultatively sexual), and the recombination rate estimates in here reflect that (e.g. they are r = rho / 2Ne, where rho was estimated directly from natural populations). To get 'true' physical recombination rate estimates, each of the values would be divided by the rate of sex, 0.001194 (explained further in the results/discussion here) which I've left as a note in the script. I figure that if simulating wild populations it makes more sense to have effective recombination rates in there as opposed to the physical rates, since that would otherwise inflate the amount of recombination happening in the simulation.

So these are still technically per-generation per-bp recombination rates (e.g. the mean_r_realized column in the figshare dataset) where the infrequency of sex is 'baked into' the values via Ne and so they are accordingly lower. I figured this was the easiest way to do handle this based on the discussion in #857.

Re: generation time, given the above calculation of 876 doublings in a year I set the generation time to 1/876 years, following how the generation time was set for E. coli (26280 doublings per year yielding a 1/26280 generation time).

updated based on comments in popsim-consortium#1067

izabelcavassim · 2021-11-02T04:20:06Z

ok @petrelharp made the edits you suggested and fixed a tiny thing on the generation time reference. I guess you can merge when you will.

petrelharp · 2021-11-02T04:39:42Z

Awesome, thanks!

izabelcavassim force-pushed the QC_Chlamydomonas_reinhardtii branch from 147b452 to ae0d988 Compare October 28, 2021 16:47

petrelharp reviewed Oct 28, 2021

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QC for Chlamydomonas reinhardtii #890

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izabelcavassim added a commit to izabelcavassim/stdpopsim that referenced this pull request Nov 1, 2021

updates

52dc0c2

updated based on comments in popsim-consortium#1067

species QC to ChlRei

c4923b7

izabelcavassim force-pushed the QC_Chlamydomonas_reinhardtii branch from 52dc0c2 to c4923b7 Compare November 2, 2021 04:18

Update tests/test_ChlRei.py

5f93436

petrelharp merged commit 0fc1dbe into popsim-consortium:main Nov 2, 2021

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species QC to ChlRei #1067

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		print("This is the mutation rate")
		print(self.genome.get_chromosome(name).mutation_rate)

species QC to ChlRei #1067

species QC to ChlRei #1067

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