Bash: use nth row as part of the command line - bash

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

Read the file in a loop:
i=1
while read -r line; do
${tool}fastQTL.1.165.linux --vcf ${vcf}GT.vcf.gz --bed pheno_bed.gz --region "$line" --permute 1000 --out "$i"_perm.txt
((i++))
done < loc_info.txt

Answer 2

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

Answer 3

Try replacing tail -n+"$i" loc_info.txt
with $(head -n $i loc_info.txt | tail -n 1)
Example
numOfLines=$(wc -l loc_info.txt | cut -d ' ' -f 1)
for i in $(seq 1 $numOfLines)
do
${tool}fastQTL.1.165.linux --vcf ${vcf}GT.vcf.gz --bed pheno_bed.gz -
-region $(head -n $i loc_info.txt | tail -n 1) --permute 1000 --out "$i"_perm.txt
done