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.
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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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
>
--
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
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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