ShortRead streamer

[bio_jit]

Hi I am using R in windows 7
I got a small program to split a large fastq file in 1 million reads/file and name them automatically. Programm running O.k. but I want to change the output folder how I do that?
my programm

FastqFile<- "./Sequencing/ERR12730_1.fastq.gz"

fileBaseName<-sub("fastq$", " ", FastqFile)

#iterate over Fastqfile

f<- FastqStreamer(FastqFile, 1000000)
file_index<-0

while(length(fq<-yield(f))){
newName<-paste(fileBaseName, "_", file_index, ".fastq", sep =" ")
writeFastq( fq, file=newName)
file_index<- file_index+1
}
close(f)

I want to send the output files in other folder say ./Sequencing/output
How to do?
Plz help me out!

[TiborNagy]

insert the following code before writeFastq:

newName <- paste('Sequencing/output', newName, sep='/')

[bio_jit]

not working!

Hi
i did as you said but getting this error now

Error in writeFastq(fq, file = newName) :
failed to open file '/Sequencing/output./Sequencing/ERR127306_1.fastq.gz_0.fastq'

any suggestions?

[TiborNagy]

Sorry, I did not realize the file name contains directory structures.

newName <- paste('Sequencing/output', basename(newName), sep='/')

The output will be: Sequencing/output/ERR12730_1.fastq.gz_0.fastq