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

Question

[Ana]

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

[h.mon]

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

Answer 1

[Alex Reynolds]

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.

Answer 2

[Zev.Kronenberg]

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

[Alex Reynolds]

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.

[Zev.Kronenberg]

Alex Reynolds No problem, see edited answer. I love how fast and sleazy perl is.

Answer 3

[ole.tange]

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}