Peter Mortensen Peter Mortensen - 5 months ago 20
Linux Question

Looping through the content of a file in Bash?

How do I iterate through each line of a text file with Bash?

With this script

echo "Start!"
for p in (peptides.txt)
do
echo "${p}"
done


I get this output on the screen:

Start!
./runPep.sh: line 3: syntax error near unexpected token `('
./runPep.sh: line 3: `for p in (peptides.txt)'


(Later I want to do something more complicated with $p than
just output to the screen.)




The environment variable SHELL is (from env):

SHELL=/bin/bash


/bin/bash --version
output:

GNU bash, version 3.1.17(1)-release (x86_64-suse-linux-gnu)
Copyright (C) 2005 Free Software Foundation, Inc.


cat /proc/version
output:

Linux version 2.6.18.2-34-default (geeko@buildhost) (gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)) #1 SMP Mon Nov 27 11:46:27 UTC 2006


The file peptides.txt contains:

RKEKNVQ
IPKKLLQK
QYFHQLEKMNVK
IPKKLLQK
GDLSTALEVAIDCYEK
QYFHQLEKMNVKIPENIYR
RKEKNVQ
VLAKHGKLQDAIN
ILGFMK
LEDVALQILL

Answer

The correct syntax is:

while read p; do
  echo $p
done <peptides.txt

Exceptionally, if the loop body may read from standard input, you can open the file using a different file descriptor:

while read -u 10 p; do
  ...
done 10<peptides.txt

Here, 10 is just an arbitrary number (different from 0, 1, 2).