Looping through the content of a file in Bash

user_63550 0
Viewed 2350238

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
io unix linux loops bash
15 Answers

This might be the simplest answer and maybe it don't work in all cases, but it is working great for me:

while read line;do echo "$line";done<peptides.txt

if you need to enclose in parenthesis for spaces:

while read line;do echo \"$line\";done<peptides.txt

Ahhh this is pretty much the same as the answer that got upvoted most, but its all on one line.

user_13583040

I like to use xargs instead of while. xargs is powerful and command line friendly

cat peptides.txt | xargs -I % sh -c "echo %"

With xargs, you can also add verbosity with -t and validation with -p

user_22510800 
#!/bin/bash
#
# Change the file name from "test" to desired input file 
# (The comments in bash are prefixed with #'s)
for x in $(cat test.txt)
do
    echo $x
done
user_29924950

This is coming rather very late, but with the thought that it may help someone, i am adding the answer. Also this may not be the best way. head command can be used with -n argument to read n lines from start of file and likewise tail command can be used to read from bottom. Now, to fetch nth line from file, we head n lines, pipe the data to tail only 1 line from the piped data. 

   TOTAL_LINES=`wc -l $USER_FILE | cut -d " " -f1 `
   echo $TOTAL_LINES       # To validate total lines in the file

   for (( i=1 ; i <= $TOTAL_LINES; i++ ))
   do
      LINE=`head -n$i $USER_FILE | tail -n1`
      echo $LINE
   done
user_25412670

Another way to go about using xargs

<file_name | xargs -I {} echo {}

echo can be replaced with other commands or piped further.

user_46706510
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