[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

[Bhagwat, Aditya]

Hi Herve,


> It feels that a coercion method from BSgenome to GRanges should rather be defined in the BSgenome package itself.

:-)


> Patch/PR welcome on GitHub.

Owkies. What pull/fork/check/branch protocol to be followed?


> Is this what you have in mind for this coercion?
> as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")

Yes.

Perhaps also useful to share the wider context, allowing your and others feedback for improved software design.
I wanted to subset a <https://support.bioconductor.org/p/124367> BSgenome (without the _random or _unassigned), but Lori explained this is not possible.<https://support.bioconductor.org/p/124367>
Instead Lori suggested to coerce a BSgenome into a GRanges<https://support.bioconductor.org/p/123489>, which is a useful solution, but for which currently no exported S4 method exists<https://support.bioconductor.org/p/124416>
So I defined an S4 coercer in my multicrispr package, making sure to properly import the Bsgenome class<https://support.bioconductor.org/p/124442>.
Then, after coercing a BSgenome into a GRanges, I can extract the chromosomes, after properly importing IRanges::`%in%`<https://support.bioconductor.org/p/124367>
Which I can then on end to karyoploteR<https://support.bioconductor.org/p/124328>, for genome-wide plots of crispr target sites.

A good moment also to say thank you to all of you who helped me out, it helps me to make multicrispr fit nicely into the BioC ecosystem.

Speeking of BioC design philosophy, can any of you suggest concise and to-the-point reading material to deepen my understanding of the core BioC software design philosophy?
I am trying to understand that better (which was the context for asking recently why there are three Vector -> data.frame coercers in S4Vectors<https://support.bioconductor.org/p/124491>)

Cheers,

Aditya




________________________________________
From: Pages, Herve [hpages using fredhutch.org]
Sent: Tuesday, September 10, 2019 6:45 PM
To: Bhagwat, Aditya; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Hi Aditya,


More generally speaking, coercion methods should be defined in a place
that is "as close as possible" to the "from" or "to" classes rather than
in a package that doesn't own any of the 2 classes involved.
Is this what you have in mind for this coercion?

> as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
GRanges object with 7 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
chrI chrI 1-15072423 *
chrII chrII 1-15279345 *
chrIII chrIII 1-13783700 *
chrIV chrIV 1-17493793 *
chrV chrV 1-20924149 *
chrX chrX 1-17718866 *
chrM chrM 1-13794 *
-------
seqinfo: 7 sequences (1 circular) from ce10 genome

Thanks,
H.


On 9/6/19 03:39, Bhagwat, Aditya wrote:
> Dear Bioc devel,
>
> Is it possible to import the BSgenome class without attaching BiocGenerics (to keep a clean namespace during the development of multicrispr<https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.gwdg.de_loosolab_software_multicrispr&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=MIR-kUeXy9oWokdQxItuG82hrvs0uwP1aBIqNdM-Jrs&e= >).
>
> BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
>
> (Posted earlier on BioC support<https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=oBSScH5uD5j0vCAaj4dfWepjiNGtHm9q5gA8eaIudZ4&e= > and redirected here following Martin's suggestion)
>
> Thankyou :-)
>
> Aditya
>
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