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how to run STRUCTURE command n times for each K value?

I am running some STRUCTURE analysis and set k = {1..10} by using this command (only 1 run for each K):

for k in seq10
do
python /home/ubuntu/bin/fastStructure/structure.py -K $k --input=../file.snps --output=snpl525D --format=str
done

Instead of 1 run for each K, now I want to get 15 runs for each K, could you please help me to modify the code above to do this job! thanks

structure bash
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updated by Zev.Kronenberg Zev.Kronenberg • written by Ana Ana

It seems to me you are overwriting the output at each loop iteration.

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written by h.mon h.mon

3 answers

Nest a per-k for loop inside a parent for loop:

$ for k in `seq 1 10`; do for eachK in `seq 1 15`; do echo "$k : $eachK"; done; done
1 : 1
1 : 2
1 : 3
1 : 4
1 : 5
...
10 : 13
10 : 14
10 : 15

As a comment notes, you may be overwriting output on each iteration. You can use the values of k and eachK to uniquely name the result.

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written by Alex Reynolds Alex Reynolds

Since perl is still cool. Here's the gist, 

perl -e 'print join "\n", (0..10)' | xargs -I {} -P 10 admixture -K {} -o {}.something

Edited:

   perl -e 'print join "\n", ((0..10) x 15)' | xargs -I {} -P 10 admixture -K {} -o {}.something
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written by Zev.Kronenberg Zev.Kronenberg

I think, but am not certain, that the question is asking how to run 15 trials on each of ten values, not necessarily how to run ten jobs in parallel.

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written by Alex Reynolds Alex Reynolds 
doit() {
  k="$1"
  n="$2"
  python /home/ubuntu/bin/fastStructure/structure.py -K "$k" --input=../file.snps --output=snpl525D-"$k"-"$n" --format=str
}
export -f doit
parallel doit ::: {1..10} ::: {1..15}
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written by ole.tange ole.tange

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