[BioC] BSgenome.Mmulatta.UCSC

Martin Morgan mtmorgan at fhcrc.org
Thu Nov 28 17:52:25 CET 2013


On 11/28/2013 07:20 AM, Brian Smith wrote:
> Hi Martin,
>
> Thanks for the reply!
>
> I get the following:
>
> --------------------------------------------------
>  > library(AnnotationHub)
>  > hub = AnnotationHub()
>  > Mmulatta2 =
> hub$ensembl.release.73.fasta.macaca_mulatta.dna.Macaca_mulatta.MMUL_1.73.dna.toplevel.fa.rz
> Warning message:
> In .getResource(x, name) : incomplete path

probably you are using a version of R for which this resource is not available. 
There is tab completion, and once you get to

hub$ensembl.release.7

press the tab key. Likely you'll see

 > hub$ensembl.release.7
hub$ensembl.release.70. ... [427]  hub$ensembl.release.72. ... [393]
hub$ensembl.release.71. ... [426]

and you can complete to

Mmullata2 = 
hub$ensembl.release.72.fasta.macaca_mulatta.dna.Macaca_mulatta.MMUL_1.72.dna.toplevel.fa.rz

Print Mmullata2 to the console to ensure that it is an 'FaFile' object.


>  > getSeq(Mmulatta2, GRanges("1", IRanges(567089, width=1)))  #A DNAStringSet
> instance of length 1
> Error in (function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘getSeq’ for signature
> ‘"character"’
>
> --------------------------------------------------
>
> Am I doing something wrong, or do I need to install another package?
>
> thanks!
>
>
> On Wed, Nov 27, 2013 at 2:33 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 11/27/2013 08:58 AM, Brian Smith wrote:
>
>         Hi,
>
>         I wanted to use the Mmulatta genome in bioconductor, but using
>         "available.genomes()", I see that only the rheMac2 (from 2006) is
>         available.
>
>         UCSC also shows rheMac3 (from 2010). Is there a way that I can
>         download/incorporate this?
>
>         Essentially, I want to find the nucleotide at specific positions in the
>         rhesus genome (e.g. chr1 - 567089).
>
>
>     Depending on what you're actually interested in,
>
>        library(AnnotationHub)
>        hub = AnnotationHub()
>        Mmulatta =
>     hub$ensembl.release.73.fasta.__macaca_mulatta.dna.Macaca___mulatta.MMUL_1.73.dna.__toplevel.fa.rz
>
>     and then
>
>      > getSeq(Mmulatta, GRanges("1", IRanges(567089, width=1)))  A DNAStringSet
>     instance of length 1
>          width seq                                               names
>     [1]     1 G                                                 1
>
>     Martin
>
>
>         thanks!!
>
>                  [[alternative HTML version deleted]]
>
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>
>     --
>     Computational Biology / Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N.
>     PO Box 19024 Seattle, WA 98109
>
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>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



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