add sus scrofa #1312 #1672
add sus scrofa #1312 #1672
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I will work with @AprilYUZhang on revising this PR (for issue #1312) and the follow-up QC. |
stdpopsim/catalog/SusScr/species.py
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| _ZhangEtAl = stdpopsim.Citation( | ||
| doi="https://doi.org/10.1016/j.gpb.2022.02.001", | ||
| year=2022, | ||
| author="Mingpeng Zhang et al.", |
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Change to author="Zhang et al.",
stdpopsim/catalog/SusScr/species.py
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| _JohnssonEtAl = stdpopsim.Citation( | ||
| doi="https://doi.org/10.1186/s12711-021-00643-0", | ||
| year=2021, | ||
| author="Martin Johnsson et al.", |
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Change to author="Johnsson et al.",
stdpopsim/catalog/SusScr/species.py
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| "16": 1.1407464686635653e-08, | ||
| "17": 1.3779949516098884e-08, | ||
| "18": 1.3679923888648167e-08, | ||
| "X": -1, |
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We should provide a value for X chromosome too. I appreciate that Johnsson et al. (2021) does not list X-chromosome recombination rate. Hence, I suggest that you calculate average recombination rate across other chromosomes (exclude Y and MT) and replace this for the X-chromosome rec rate value. Make this calculation clear in the code here.
stdpopsim/catalog/SusScr/species.py
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| # citation is optional and can be deleted if not needed.] | ||
| citations=[ | ||
| stdpopsim.Citation( | ||
| author="", year=-1, doi="", reasons={stdpopsim.CiteReason.ASSEMBLY} |
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@AprilYUZhang provide reference for the pig genome assembly that we use here
stdpopsim/catalog/SusScr/species.py
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| common_name="Pig", | ||
| genome=_genome, | ||
| ploidy=2, | ||
| # The age at first pregnancy varies in the wild from about 10 to 20 months, |
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@AprilYUZhang cite the paper here in the comments and point to page/figure/table for there estimates
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Sorry, I have no idea; this sentence is from the explanation of generation time. Should I write "the details see in _ZhangEtAl"?
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Point to where in the paper is this detail, say page
stdpopsim/catalog/SusScr/species.py
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| author="Martin Johnsson et al.", | ||
| reasons={stdpopsim.CiteReason.REC_RATE}, | ||
| ) | ||
| # [The following are notes for implementers and should be deleted |
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@AprilYUZhang cite the paper here in the comments and point to page/figure/table for there estimates
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@AprilYUZhang I left some comments for you to address. I will then have another look. Thanks for this addition to the stdpopsim catalogue!
stdpopsim/catalog/SusScr/species.py
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| "MT": 0, | ||
| } | ||
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| # the de novo mutation rate is inferred by Mingpeng Zhang et al 2022, |
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@AprilYUZhang point to page/figure/table for there estimates from Zhang et al
…us_scrofa pull remote, becase remote have been updated
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1672 +/- ##
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Coverage 99.85% 99.85%
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Files 136 139 +3
Lines 4690 4718 +28
Branches 470 470
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+ Hits 4683 4711 +28
Misses 3 3
Partials 4 4 ☔ View full report in Codecov by Sentry. |
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I advised @AprilYUZhang offline on this implementation, which is now very complete, and I volunteer to QC it. I have a question though about recombination rate averaging. The information on the recombination rate for this species comes from a study with an extensive pedigree (so we deem it's very good) and the study reported the recombination rate per Mb of each autosome. To get a value for the X chromosome, @AprilYUZhang has:
I think this makes sense, but would like to hear from others here what you have done in such cases. I think that weighted average to represent the recombination rate per basepair for the genome is the right thing to do (average of ratios ...). But is this the right value to use for the X chromosome (in the absence of other information) or should one use the simple (unweighted) average. It's a minor detail, but I thought I would ask here. Otherwise, I think this looks very good @AprilYUZhang and could soon be merged in by the maintainers. You will have to squash the commits before this happens though! @AprilYUZhang is also looking at adding the recombination map and demographic models later. |
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Weighted average is consistent with what we do elsewhere - sounds good! |
| # which is roughly equivalent to the average age of | ||
| # the first pregnancy in sows and the beginning of rut in boars | ||
| # plus the pregnant gestation period of sows." | ||
| generation_time=3, |
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Hm - generation time isn't the average age of first pregnancy of an individual, it's the average age of a parent at time of birth of their child, i.e., the thing you'd get by picking a random individual and asking how old their parent was when they were born. For instance, human generation time is 25-30 years (estimates vary).
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@petrelharp your are totally right, but this is verbatim text from the paper that we are following, so I guess we stick to their 3 years, which is an OK value.
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Um, I guess? I mean, according to the stated rationale, that explanation is an underestimate, probably by a good factor, unless most pigs die after one litter.
This paper used 5 years, which the paper you're citing cites several other papers as using? Hm, that's "based on a studbook"; I wonder what the method is?
However, googling suggests that a mean life span is like 4-8 years; so 3 can't be too far off (maybe just a factor of 2). If you do want to use this one, then make sure you document that it is not the actual generation time.
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Looks good! Just a thing about the generation time. |
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