To loop files and run in mutiple times

Question

[muralinmars]

Hi guys,

It will be great if someone can give some suggestions.

How to loop the body (shown below) to different "chr$" files, where dollar sign take different values (eg. 1,3,5,7,12).

Say for instance, for the first run it takes the value chr1 (and use it in the body) and then chr3 and so on.....

This is the body of the loop file:

/drn/common/u/snn/FAST/FAST.1.8.mc/bin/linux_x86_64/FAST \
       --summary-file /drn/common/data/chr$.simple \
       --hap-file /drn/common/CEU/chr$.hap.gz \
       --pos-file /drn/common/CEU/chr$.hap.ra.gz \
       --out-file /drn/common/output/out_chr$ \
       --gene-set /drn/common/data/chr$.txt \
       --chr $ \
       --mode summary \
       --n-sample 2000 \
       --logistic-vegas-perm \

Thanks a bunch

Answer 1

[Ashutosh Pandey]

Save the following text as a shell file (test.sh) and run it.

​for i in 1 3 5 7 2
do
    command = `/drn/common/u/snn/FAST/FAST.1.8.mc/bin/linux_x86_64/FAST \
                         --summary-file /drn/common/data/chr"$i".simple \
                         --hap-file /drn/common/CEU/chr"$i".hap.gz \
                         --pos-file /drn/common/CEU/chr"$i".hap.ra.gz \
                         --out-file /drn/common/output/out_chr"$i"\
                         --gene-set /drn/common/data/chr"$i".txt \
                         --chr "$i"\
                         --mode summary \
                         --n-sample 2000 \
                         --logistic-vegas-perm`
    echo $command
done

[Devon Ryan]

I should have refreshed before posting, you beat me by 3 minutes!

[muralinmars]

Thanks a bunch,, ashutosh,

what does the echo $command do - just curious

[Devon Ryan]

It prints the command that you want to run to the screen to ensure that things are working correctly.