How to make work the following script? I got this code from some tutorial and I have no idea how to make it work? Is it a perl script or python? how to execute it. Kindly help me out in this regard . Thanks
$ for left_fq in /data/reads/NA19240/*_1.fq; do
$ right_fq=${left_fq/_1.fq/_2.fq}
$ lane_id=$(basename ${left_fq/_1.fq})
$ rtg format -f fastq -q sanger -o ${lane_id} -l ${left_fq} -r $
{right_fq} --sam-rg "@RG\tID:${lane_id}\tSM:NA19240\tPL:ILLUMINA"
$ done
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written
by
adnan.haider.ra •
Hi Adnan,
As Pierre says, it is bash script.
To fully understand it, you should first get some insights of linux bash commands, such ls, cd. Supposing you are following a tutorial, you should have some .fq files at /data/reads/NA19240/. They should name as *_1.fq and *_2.fq. And you should have a software called rtg, which may mentioned in the tutorial.
Then you should be able to run it.
To run, either type the whole following code in command line:
for left_fq in /data/reads/NA19240/*_1.fq; do right_fq=${left_fq/_1.fq/_2.fq}; lane_id=$(basename ${left_fq/_1.fq}); rtg format -f fastq -q sanger -o ${lane_id} -l ${left_fq} -r ${right_fq} --sam-rg "@RG\tID:${lane_id}\tSM:NA19240\tPL:ILLUMINA"; done
or: type for left_fq in /data/reads/NA19240/*_1.fq; do then press "Enter" or "Return" on your keyboard. And do the same for the following lines. IGNORE the $ signs at the start of each line. It is just the sign indicating that you should run the rest part in your command line.
Hope this can help you.
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written
by
Roden Luo •
Sorry. This reply presumes that you can try this on a Linux or Unix machine. And if you are going to use some other bioinformatics tools. I highly suggest that you use Linux to follow those tutorials. You can try Ubuntu, it is a free system.
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it looks like shell script / bash
Hmm . Can you kindly elaborate a little more? like how can i make this script work? pasting in notepad? .bat extension?
"Is there a way to run Bash scripts on Windows?" http://stackoverflow.com/questions/6413377
Oh, I did not notice you may use windows. That would be very complicated I think.