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@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?
> Thanks,
> Michael
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

