Proposed contribution task for Outreachy applicants: Register UCSC genome gorGor6

[hpages]

gorGor6 is the latest UCSC genome for Gorilla (Gorilla gorilla gorilla). 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 Gorilla in the UCSC species tree on the left, click on it, then make sure to select the latest Gorilla Assembly (gorGor6). This will display a bunch of additional information about the gorGor6 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 that getChromInfoFromUCSC() still works on an unregistered genome, but in "degraded" mode, that is:

• the assembled.molecules argument is ignored,
• the assembled and circular columns of the returned data.frame are filled with NAs,
• and the chromosomes/sequences are not returned in any particular order.

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 a README.TXT file that provides some brief information about what a "registration file" should contain (unfortunately the registration process is not fully documented).

For gorGor6, since this is the first gorGor genome that we're going to register in GenomeInfoDb, we need to start the gorGor6.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 the NCBI_LINKER component for now. We'll add it later, once the corresponding NCBI assembly (Kamilah_GGO_v0) is also registered (registering Kamilah_GGO_v0 is the topic of issue #61).

IMPORTANT NOTES TO OUTREACHY APPLICANTS:

• Make sure to complete all the Preliminary tasks listed here before you start working on this task. In particular, make sure that you have R 4.2 and that you are set up to use the devel version of Bioconductor (currently 3.16).
• Only one applicant can work on this task. If you choose to work on this task, please make sure to assign yourself so other applicants know that the task is already being worked on. If later on you change your mind, please unassign yourself. It's ok to change your mind!
• To work on this task, please fork the GenomeInfoDb repository. Then do your work on that fork.
• Always test your changes before you commit them to your fork. This consists in installing the modified package, starting R, loading the package, and playing around with the new functionality. This process is called "ad hoc manual testing". Once everything behaves and looks as expected, run R CMD build and R CMD check on the package. Note that R CMD check should always be run on the source tarball produced by R 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!
• Once your work is ready to be merged, please submit a PR (Pull Request).
• Remember to record your contribution on Outreachy at https://www.outreachy.org/outreachy-december-2022-internship-round/communities/bioconductor/refactor-the-bsgenomeforge-tools/contributions/.

[hpages]

I have completed all the preliminary tasks

Great!

I just assigned you to this issue. Do not hesitate to ask questions, I'll do my best to help.

[Priceless-P]

Hi @hpages, Can I work on this issue once I'm done with this ?

[hpages]

@kakopo PR #88 merged, thanks!