Shell script to read variables from file and use that in perl script

Question

I want to write a shell script, that reads a file and use the columns of that file as input for a perl script. The perl script is going through files (number1, number2), pulls out the ID and write those to a new file. The perl script is working fine if I use it with the command line, however, my question is how I write a shell script to use the variables in my input_file for the perl script.

My input_file looks like

number1 ID1
number2 ID2

And I use the following shell script (which is not working, so please help with this)

#!/bin/bash

input_file="$1" 

while IFS=" " read -r number ID
do
    perl extract.pl $ID $number.ext > $number_ID.ext
done < "$1"

Please take a look: shellcheck.net

Cyrus
– Cyrus

2017-12-18 07:46:09 +00:00
Commented Dec 18, 2017 at 7:46 — Cyrus
– Cyrus, Commented Dec 18, 2017 at 7:46
Great site, I did not know it. Thanks!

Gravel
– Gravel

2017-12-18 09:14:08 +00:00
Commented Dec 18, 2017 at 9:14 — Gravel
– Gravel, Commented Dec 18, 2017 at 9:14

Cyrus · Accepted Answer · 2017-12-18 08:03:57Z

2

Replace

$number_ID.ext

with

${number}_ID.ext

_ is a character allowed in variable names. That's why bash is looking for $number_ID. . is not allowed.

edited Dec 18, 2017 at 8:03

answered Dec 18, 2017 at 7:44

Cyrus

90.2k15 gold badges112 silver badges173 bronze badges

Sign up to request clarification or add additional context in comments.

1 Comment

tripleee Over a year ago

Maybe also point out (like shellcheck.net already does) that input_file is assigned but unused.

Collectives™ on Stack Overflow

Shell script to read variables from file and use that in perl script

1 Answer 1

1 Comment

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

1 Comment

Your Answer

Sign up or log in

Post as a guest

Related