Question: Looping over plink files
0
gravatar for paolo002
6 months ago by
paolo002140
paolo002140 wrote:

Hi, I have .bed .bim. fam files for various chromosomes of some individuals and I would like merge with other plink files of some other individuals again for each chromosomes I would like to write a loop that does the merging automatically for all the files in just one command line Something like this:

for file in /home/users/chrs/*.{bed,bid,fam};
do plink --bfile filename1.chr$ --bmerge filename2.chr$.bed filename2.chr$.bim filename2.chr$.fam --out filename1_filename2_merged;
done

Here $ means any number from 1 to 22 for each files of the chromosomes.

Any help will be highly appreciated,thanks

linux bash shell • 396 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by paolo002140

you need another inner loop: for j in seq 1 22

ADD REPLYlink written 6 months ago by Santosh Anand4.7k

I see, but about the $ sign, it is ok to write like this?will it take any number from 1 to 22 ?

ADD REPLYlink written 6 months ago by paolo002140
for j in $(seq 1 22); do echo chr$j; done
ADD REPLYlink written 6 months ago by Santosh Anand4.7k

Hi, sorry, I tried the two loops but it did not work, can you be more specific please?

ADD REPLYlink written 6 months ago by paolo002140

Could you write what did you try?

ADD REPLYlink written 6 months ago by Santosh Anand4.7k

I see,I have got it Thanks

ADD REPLYlink written 6 months ago by paolo002140

Did you try --merge-list option from plink ? You can merge all the chormosomes for one file using this and do a for loop to merge with other files. http://zzz.bwh.harvard.edu/plink/dataman.shtml#mergelist

ADD REPLYlink modified 6 months ago • written 6 months ago by Inquisitive899560
1

I see, yes, I know about that option but I have not tried it. I will do that then. Cheers

ADD REPLYlink written 6 months ago by paolo002140
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