[BioC] XstringViews and Fasta

[Droit Arnaud]

Hello,

I am using XstringViews object to transform bed file to fasta file :

as(chr, "XStringViews")
TopSeq<<-Views(chr, start=start, end=end,names=as.character(i))
write.XStringViews(TopSeq, file=paste("BED","_TEST_QUEST",".",method,as.character(nTop),"_",i,".fa",sep=""), format="fasta", width=10000)

Example :

>TopSeq
  Views on a 242951149-letter DNAString subject
subject: CGTATCCCACACACCACACCCACACACCACACCC...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
views:
        start       end width
[1] 162681889 162682089   201 [TATGTGAAATTTACATTCCATGA...TCCTTGAAGTTAGGAGCAACTT]

I cannot get only fasta sequence into variable. I am wondering if it possible to get sequence into variable.

Thanks

Arnaud Droit.