Changing character in a for loop in bash script to execute a program many times

Question

I am new to bash scripting and would like to call a program 22 times. for 22 different files.

file names look something like this: filename_chr1_test filename_chr2_test filename_chr3_test ... filename_chr22_test

this is my for loop so far:

#!/bin/bash

for chr_num in {1:22}:
    do
       /path/to/plink --file filename_chr$chr_num_test --exampletest
    done

For some reason I'm getting an error back. I'm not exactly sure why. Can someone help me debug?

Thanks for your help!!

1: for chr_num in {1..22} 2: Use ${chr_num} instead of $chr_num so that the interpreter will work correctly.. — Code4aliving
– Code4aliving, Commented Apr 14, 2017 at 17:11
@BradBales Hi brad. OH! Do I include ( ) around chr_num in the for loop statement AND in where I list the file name? — Sheila
– Sheila, Commented Apr 14, 2017 at 17:12

Cyrus · Accepted Answer · 2017-04-14 17:12:56Z

3

I suggest:

#!/bin/bash

for chr_num in {1..22}; do
  /path/to/plink --file filename_chr${chr_num}_test --exampletest
done

answered Apr 14, 2017 at 17:12

Cyrus

90.2k15 gold badges112 silver badges173 bronze badges

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

Comments

chepner · Accepted Answer · 2017-04-14 18:17:17Z

3

Don't use brace expansion; use a C-style for loop:

for((i=1;i<=22;i++)); do
  /path/to/plink --file filename_chr${chr_num}_test --exampletest
done

This doesn't require the entire sequence to be expanded in memory at once (not a big deal for a short sequence).

answered Apr 14, 2017 at 18:17

chepner

538k77 gold badges594 silver badges746 bronze badges

3 Comments

Cyrus Over a year ago

I suggest to replace three i by chr_num or one chr_num by i.

Sheila Over a year ago

Thanks @chepner - what is the motivation to use a C-style loop over brace expansion?

that other guy Over a year ago

@Sheila The main benefit is that you don't have to hard code the number. You can do n=42; for ((i=1; i<=n; i++)) but you can't do for i in {1..n} . It's also more efficient once you start counting to thousands or millions

Collectives™ on Stack Overflow

Changing character in a for loop in bash script to execute a program many times

2 Answers 2

Comments

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related