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

Wed Sep 11 12:24:45 CEST 2019

Hi Aditya,

On 9/11/19 01:31, Bhagwat, Aditya wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>BSgenome 
> (without the _random or _unassigned), but Lori explained this is not 
> possible. 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=> 
> 
> Instead Lori suggested to coerce a BSgenome into a GRanges 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123489&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=6Eh73QthFfpPsfpRdPWs98pH6GHvv1Z23ORp34OCPxA&e=>, 
> which is a useful solution, but for which currently no exported S4 
> method exists 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124416&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=H8owJlOQrNHwNFHfCxGHe27Jxu6xjxpuAMWK8JlTU4Y&e=>
> So I defined an S4 coercer in my multicrispr package, making sure to 
> properly import the Bsgenome class 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=2XNBVcwoJTjlxY_gl4UPzrHPKmKH9LTnM4ih5SQOfps&e=>.
> Then, after coercing a BSgenome into a GRanges, I can extract the 
> chromosomes, after properly importing IRanges::`%in%` 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>

Looks like you don't need to coerce the BSgenome object to GRanges. See 
https://support.bioconductor.org/p/123489/#124581

H.

> Which I can then on end to karyoploteR 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124328&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=M90_rBO1oohGnXe2XBpQHQriFNthY_W0hzN6KWlf2S4&e=>, 
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124491&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=nBHdQoTrd1Mfu4VTMgtkPyUQ0Ju2NLeX-0X1Ny3fSeg&e=>)
> 
> 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
>  >
>  > [[alternative HTML version deleted]]
>  >
>  > _______________________________________________
>  > Bioc-devel using r-project.org mailing list
>  > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=cEojiObibdSuzmh21opvy85DZyRrjtfo1vEMopKWmAg&e=
>  >
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319