How to pass parameters to a command in bash when run line by line? - bash

Question

I have a file of parameters which I want to feed into a command in bash. Please note that I write the command below but the question isn't about the command, it's about how to pass the parameters from this file into the command.
The file, myfile.txt, looks like this:
3 rs523534 62297313 63097313
4 rs6365365 375800230 376600230
8 rs75466 63683994 64483994
I have a script to read each line and feed it into a command:
while read -r line; do
plink --bfile mydata \
--chr echo $line | awk '{print $1}' \
--from-bp echo $line | awk '{print $3}' \
--to-bp echo $line | awk '{print $4}' \
--r2 \
--ld-snp echo $line | awk '{print $2}' \
--ld-window-kb 100000000 \
--ld-window 100000000 \
--ld-window-r2 0 \
--out echo "processing/5_locuszoom/$line" | sed 's/ /_/g'
done < "myfile.txt"
This doesn't work:
awk: fatal: cannot open file `--to-bp' for reading (No such file or directory)
awk: fatal: cannot open file `--from-bp' for reading (No such file or directory)
awk: fatal: cannot open file `--r2' for reading (No such file or directory)
awk: fatal: cannot open file `--ld-window-kb' for reading (No such file or directory)
But if I run it manually, e.g.
plink --bfile mydata \
--chr 3 \
--from-bp 62297313 \
--to-bp 63097313 \
--r2 \
--ld-snp rs523534 \
--ld-window-kb 100000000 \
--ld-window 100000000 \
--ld-window-r2 0 \
--out 3_rs523534_62297313_63097313
It works fine.
Is there a way that I can better feed the variable information into the command so that it works?

Answer 1

If you want to run a command inline to another command, you need to use a command substitution. So instead of --chr echo $line | awk '{print $1}' \ for example, you'd write --chr $( echo $line | awk '{print $1}' ) \.
But in this case it's not necessary, since read can already split the data for you.
#!/bin/bash
while read -r arg1 arg2 arg3 arg4 ; do
<do things with your args here>
done <"myfile.txt"
read will split each line based on the contents of IFS and populate each name you give it with the corresponding token from the split line.

Answer 2

Probably what you want is, in pure bash
#!/bin/bash
while read -ra args; do
out="${args[*]}"
plink --bfile mydata \
--chr "${args[0]}" \
--from-bp "${args[2]}" \
--to-bp "${args[3]}" \
--r2 \
--ld-snp "${args[1]}" \
--ld-window-kb 100000000 \
--ld-window 100000000 \
--ld-window-r2 0 \
--out "processing/5_locuszoom/${out// /_}"
done < "myfile.txt"
Use of awk and sed for this task is superfluous.