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

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?

CodePudding user response：

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.

CodePudding user response：

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.