[BioC] How to get sequences corresponding to a GRanges?

[Cei Abreu-Goodger]

Thanks Martin, that's exactly what I was looking for! (missed the 
showMethods("getSeq"), sorry)


On 10/28/12 5:49 PM, Martin Morgan wrote:
> On 10/28/2012 11:28 PM, Cei Abreu-Goodger wrote:
>> Hello all,
>>
>> I was wondering if there was a simple way to get the sequences
>> corresponding to
>> the ranges stored in a GRanges object. If you have the original
>> sequences in a
>> BSgenome object, you can use 'getSeq'. But what if you just have the
>> fasta file,
>> imported as a DNAStringSet object?
>>
>> I want to avoid having to forge a new BSgenome object each time, since
>> I'm
>> dealing with unfinished assemblies, with thousands of sequences that I
>> don't
>> want to split into individual fasta files, etc.
>
> Rsamtools has FaFile and FaFileList to represent (indexed, via indexFa)
> fasta files, and a getSeq method that takes an FaFile and a GRanges (or
> similar) object. This is built on top of scanFa. See
>
>    library(Rsamtools)
>    method?"getSeq,FaFile"
>
> Martin
>
>>
>> Many thanks,
>>
>> Cei
>>
>
>

-- 
Dr. Cei Abreu-Goodger
Profesor Investigador
Langebio CINVESTAV
Tel: (52) 462 166 3006
cei at langebio.cinvestav.mx

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