[BioC] getSeq on a GRangesList

[Martin Morgan]

On 06/22/2011 04:43 PM, Michael Lawrence wrote:
> I think you want something like extractTranscriptsFromGenome(). It would be
> nice if getSeq delegated to that for GRangesList.
>
> Michael
>
> On Wed, Jun 22, 2011 at 8:58 AM, Michael Cho<remhc at channing.harvard.edu>wrote:
>
>> Hi,
>>
>> I'm trying to grab sequence from a GRangesList.  Each GRanges element has
>> several sequences which I am concatenating together and using to write a
>> fasta file (with the name of the GRanges as the name of the fasta
>> sequence).
>> I can't seem to figure out a better / faster way than to loop like this:
>>
>> seq<-getSeq(Hsapiens,myGRangesList[[i]],as.character=FALSE)
>> writeFASTA(paste(seq,collapse=""), file="myOutput.fasta",
>> desc=names(myGRangesList[i]), append=TRUE)
>>
>> Any thoughts?

maybe for some GRangesList grl

seqs <- getSeq(Hsapiens, unlist(grl, use.names=FALSE),
                as.character=TRUE)
elt <- rep(names(grl), elementLengths(grl))
sapply(split(seqs, elt), paste, collapse="")

optionally wrapping the final line in DNAStringSet(). There is just one 
call to getSeq. Working on character() in the sapply / split / paste 
would seem to avoid a lot of S4 class construction overhead. I'll also 
mention scanFa / getSeq,FaFile-method in the devel version of Rsamtools, 
which one might use if the original sequence were coming from a fasta 
file rather than BSgenome.

Martin


>> Thanks,
>> Michael
>>
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>>
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