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

Martin Morgan Sun, 25 Sep 2011 18:17:41 -0700

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

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

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