[BioC] how to write fasta file of RNA sequences

Steve Lianoglou mailinglist.honeypot at gmail.com
Sun Mar 18 21:00:16 CET 2012


On Sun, Mar 18, 2012 at 3:49 PM, wang peter <wng.peter at gmail.com> wrote:
> dear all:
>         it seems writeFasta can not allow RNA sequences.
> writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA")
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "writeFasta", for
> signature "RNAStringSet"


For now, Biostrings::write.XStringSet (which writeFasta calls
internally) handles it.

Not sure if it's intentional to not support RNA* in the ShortRead
functions[*] but you can at least use Biostrings::write.XStringSet to
do what you need for now.


[*] maybe it is intentional since no sequencers I know of will read a
"U" as most (all) incorporate dNTPs (not rNTPs) while reading ... just
stabbing at the dark on this one, though.

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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