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Proposed contribution task for Outreachy applicants: Register UCSC genome xenTro10 #46
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Hello @hpages. I'd like to contribute towards this issue. I have completed the preliminary tasks. |
Hi @kakopo , please choose a task in the Cat group instead. See https://github.com/Bioconductor/BSgenomeForge/wiki/List-of-contribution-tasks-for-the-Outreachy-application-period Thanks! |
Good day sir. I love to be assigned to this task |
Hi @hpages. i just started working on it since i was going to be assigned to this task.
After installing
please what could be the cause? |
Hi @Simplecodez, I've just assigned you to this issue. Before I answer your question above, I'll take a look at the PR you submitted for the previous task (PR #69). Thanks for your patience. |
Alright sir. Thank you |
Hi @hpages please I am waiting for your response sir. |
Hi @Simplecodez ,
As I said, before moving to this new task, I wanted that we finish the previous one first. Thanks for understanding.
To work on this task, it's best to run the code in your As documented in the Make sure that all the Then try to call To understand why this error happens, we're going to run the code in the So let's get started:
When you execute this last line, the error should happen again. This tells us that the error happens in the Now let's run the code in the
This is our first deep dive in real R code. There's a lot going on with the above code so it's going to be a great learning experience. Do not hesitate to ask if you have questions. I'll do my best to help. |
Thank you very much for this explanation. I got a lot of insights as to how the code works. |
I don't know if the UCSC folks included the X chromosome or not. It could be that they didn't. If you don't see it in |
Yes I didn't see it in the seqlevels. So should I exclude it? |
Good day sir. I just created a PR now on this issue. I will be anticipating your feedback |
Thanks for the PR @Simplecodez. It looks good. For the sake of keeping the PR focused on the precise task described at the top of this issue, can you please remove the Thanks again. |
Okay sir, I have removed the NCBI linker component. |
Perfect @Simplecodez, thanks! I just merged PR #71. Next task in your group is issue #48. Whenever you are ready, go there and ask to be assigned. |
Thank you very much sir |
xenTro10
is the latest UCSC genome for the Western clawed frog (Xenopus tropicalis). See "List of UCSC genome releases" at https://genome.ucsc.edu/FAQ/FAQreleases.html for all the genomes currently supported by UCSC.Also check out the "Genome Browser Gateway" page here. This is the main entrance to the "UCSC Genome Browser". Find X. tropicalis in the UCSC species tree on the left, click on it, then make sure to select the latest X. tropicalis Assembly (
xenTro10
). This will display a bunch of additional information about thexenTro10
assembly.Note that many UCSC genomes are already registered in the GenomeInfoDb package (83 as of October 2022). The
registered_UCSC_genomes()
function in GenomeInfoDb returns the list of all the UCSC genomes that are currently registered in the package. An important thing to be aware of is thatgetChromInfoFromUCSC()
still works on an unregistered genome, but in "degraded" mode, that is:assembled.molecules
argument is ignored,assembled
andcircular
columns of the returned data.frame are filled withNA
s,Registering a genome fixes that. In other words, once a genome is registered in GenomeInfoDb, the information returned by
getChromInfoFromUCSC()
for that genome is guaranteed to be complete and accurate.See
?getChromInfoFromUCSC
(after loading GenomeInfoDb) for more information.Registering a new UCSC genome is only a matter of adding a new file, called "registration file", to
GenomeInfoDb/inst/registered/UCSC_genomes/
. Note that the folder contains aREADME.TXT
file that provides some brief information about what a "registration file" should contain (unfortunately the registration process is not fully documented).For
xenTro10
, since this is the firstxenTro
genome that we're going to register in GenomeInfoDb, we need to start thexenTro10.R
file from scratch. However, looking at other registration files to get a feeling of how things are done is always a good idea. Don't bother with theNCBI_LINKER
component for now. We'll add it later, once the corresponding NCBI assembly (UCB_Xtro_10.0
) is also registered (registeringUCB_Xtro_10.0
will is the topic of issue #47).IMPORTANT NOTES TO OUTREACHY APPLICANTS:
R CMD build
andR CMD check
on the package. Note thatR CMD check
should always be run on the source tarball produced byR CMD build
.R CMD check
might produce some NOTEs and even some WARNINGs. These are ok if they existed before your changes. You can check that by taking a look at the daily report produced by our automated builds here: https://bioconductor.org/checkResults/devel/bioc-LATEST/ Make sure to not introduce new NOTEs or WARNINGs!The text was updated successfully, but these errors were encountered: