How to code for iterating through multiple files in linux? - linux

Question

I have code which I am trying to update from another example. The aim is to run plink using files of: each chromosome, snp ids, and a file containing only 1 ID which is an individual's ID. Running these files in plink ultimately makes a vcf file per individual for a given chromosome.
I have 22 chromosome files, 1 snp file (which is always the same), and 500 individual files. For each individual I am aiming to make a vcf for each chromosome, so I have 22*500 (11000) vcf files as output.
With doing this at the moment I have tried a bash script with this:
ID=$SGE_TASK_ID
indiv=$SGE_TASK_ID
plink --bed chr${ID}.bed --bim chr${ID}.bim --fam chr${ID}.fam --extract snps.txt
--recode vcf-iid --out output${indiv}chr${ID}vcf --keep-fam individual${indiv}.txt
This runs, however it only runs through 1 individual, giving me 22 chromosome vcf files for that one person, and stops there. How do I make this run for all 500 people, would it be with a for loop? Looking through other questions I haven't been able to find one that matches my question and is in linux, any help would appreciated.
${indiv} would just be a number, so the text file that runs looks like individual1.txt and increases through the 500 individuals (individual1.txt, individual2.txt, individual3.txt)

Answer 1

Assuming that ${indiv} contains no spaces,
for indiv in $(<individuals.data); do
plink [...] individual${indiv}.txt
done
The file individuals.data would name the individuals, separated by spaces or newlines.
If unsure what the Bash shell's $(<...) operator does, try this:
for A in $(<individuals.data); do
echo "[$A]"
done
Note that, as #Kaz has observed, if wish your script to work also in shells other than Bash, then you might write $(cat ...) rather than $(<...)