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

[Pages, Herve]

Hi Aditya,

It feels that a coercion method from BSgenome to GRanges should rather 
be defined in the BSgenome package itself. Patch/PR welcome on GitHub. 
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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> 
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-- 
Hervé Pagès

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