[BioC] XStringViews with strand?

[Cei Abreu-Goodger]

Hi Herve,

Thanks for the info. I'll check out the devel version soon, and I guess 
I'll be doing something like what you suggest:

myDNAStringSet <- as(myViews, "DNAStringSet")

myDNAStringSet[strands == "-"] <- 
reverseComplement(myDNAStringSet[strands == "-"])

Cheers,

Cei

Hervé Pagès wrote:
> Hi Cei,
> 
> Cei Abreu-Goodger wrote:
>> Hi all,
>>
>> I'm trying to read in a fasta sequence, extract the "gene sequences" 
>> and write these out to a fasta file. I can read the sequences with 
>> read.DNAStringSet(), obtain an XStringViews object with Views(), but 
>> I'm having trouble knowing how to obtain the reverse complement 
>> sequence for the genes on the "-" strand. I can get them with a 
>> reverseComplement()
>> of the XStringViews object, but I can't overwrite the elements of this 
>> object. So my solution involves dealing separately with all the genes 
>> on the "+" strand and those on the "-" strand. Is there an easier way?
>>
>> An example:
>>
>> file <- system.file("extdata", "someORF.fa", package="Biostrings")
>> x <- read.DNAStringSet(file, "fasta")[[1]]
>>
>> names   <- c("a","b","c")
>> starts  <- c(10,384,947)
>> ends    <- starts+20
>> strands <- c("+","-","+")
>>
>> myViews <- Views(x, start=starts, end=ends)
>> names(myViews) <- names
>>
>> revViews <- reverseComplement(myViews[strands=="-"])
>> posViews <- myViews[strands=="+"]
> 
> Yes it has to be done separately. The content of a view cannot be modified
> because that would mean modifying the underlying subject so you would end
> up with a subject that is a mix of + and - strand. And what should be done
> when 2 views overlap, 1 being associated with a gene on the + strand and
> the other one with a gene on the - strand?
> 
> In the near future we will support replacement of the elements of a 
> DNAStringSet
> object through "[<-" and "[[<-". Then it will be possible to 
> reverseComplement
> some of its elements with something like this:
> 
>   x[strands == "-"] <- reverseComplement(x[strands == "-"])
> 
> But that will be for XStringSet only, not for XStringViews.
> 
> These developments will take place in the devel version of Biostrings in 
> the
> next few weeks.
> 
> Cheers,
> H.
> 
> 
>>
>>
>> Many thanks,
>>
>> Cei
>>
>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices datasets  utils     methods
>> [8] base
>>
>> other attached packages:
>> [1] Biostrings_2.12.1 IRanges_1.2.2     Biobase_2.4.1
>>
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> 


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