Bash: use nth row as part of the command line

Question

I am trying to use a tool called fastqtl, but it's probably less relevant here. I am interested in assigning each row of the "loc_info.txt" into the options. I wrote the following commands but it bounced back as "Error parsing command line :unrecognised option '-n+1'

Is there a way that I can make the fastQTL read and use that 1 line from "loc_info.txt" each time it runs the function?

Thanks for any suggestions!!

#!/bin/bash

tool="/path/FastQTL-2.165.linux/bin/"
vcf="/path/vcf/"
out="/path/perm_out"

for i in {1..1061}
do
${tool}fastQTL.1.165.linux --vcf ${vcf}GT.vcf.gz --bed pheno_bed.gz --region tail -n+"$i" loc_info.txt --permute 1000 --out "$i"_perm.txt
done

Answer 1

You can use a subshell for this, if you want to use the output from one command within another command so something like:

cmd1 -option $(cmd2)

here you're using the cmd2 output as input in cmd. The key here is '$' and the subshell '()'. So the solution might be:

#!/bin/bash
tool="/path/FastQTL-2.165.linux/bin/"
vcf="/path/vcf/"
out="/path/perm_out"

for i in {1..1061}
do
${tool}fastQTL.1.165.linux --vcf ${vcf}GT.vcf.gz --bed pheno_bed.gz --region $(tail -n+"$i" loc_info.txt) --permute 1000 --out "$i"_perm.txt
done