[Bioc-sig-seq] how to write a fasta file

[Martin Morgan]

On 09/25/2011 04:25 PM, wang peter wrote:
> hi every one:
>
> i read fastq file and save them as fasta
> but falied
>
> fastqfile="unmapped"
> library(ShortRead)
> reads<- readFastq(fastqfile)
> seqs<- sread(reads)
> ids<- id(reads)
>
> writeFasta(seqs, file="unmapped.fa")
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "writeFasta", for
> signature "DNAStringSet"

Hi,

     > library(ShortRead)
     > showMethods(writeFasta)
     Function: writeFasta (package ShortRead)
     object="ShortRead"

so

     writeFasta(reads, file="unmapped.fa")

or from ?writeFASTA's section See also:

     write.XStringSet(seqs, file="unmapped.fa")



>
> writeFASTA(seqs, file="unmapped.fa")
> Error in for (rec in x) { : invalid for() loop sequence
>
> what is the problem
> thank you
>
> shan gao
>
> 	[[alternative HTML version deleted]]
>
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