[BioC] XstringViews and Fasta

[Patrick Aboyoun]

Arnaud,
Could you provide more description, or code, for your situation? In particular what does "I cannot get only fasta sequence into variable. I am wondering if it possible to get sequence into variable." mean? In your code below, TopSeq is an XStringViews object. If you use the DNAStringSet constructor, you can create a DNAStringSet by DNAStringSet(TopSeq). Is that what you are looking to create in R?


Patrick




Droit Arnaud wrote:
> 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.
>
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