Looping through the content of a file in Bash

Question

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 1

cat peptides.txt | while read line
do
   # do something with $line here
done

Answer 2

@Peter: This could work out for you-

echo "Start!";for p in $(cat ./pep); do
echo $p
done

This would return the output-

Start!
RKEKNVQ
IPKKLLQK
QYFHQLEKMNVK
IPKKLLQK
GDLSTALEVAIDCYEK
QYFHQLEKMNVKIPENIYR
RKEKNVQ
VLAKHGKLQDAIN
ILGFMK
LEDVALQILL

Answer 3

Here is my real life example how to loop lines of another program output, check for substrings, drop double quotes from variable, use that variable outside of the loop. I guess quite many is asking these questions sooner or later.

##Parse FPS from first video stream, drop quotes from fps variable
## streams.stream.0.codec_type="video"
## streams.stream.0.r_frame_rate="24000/1001"
## streams.stream.0.avg_frame_rate="24000/1001"
FPS=unknown
while read -r line; do
  if [[ $FPS == "unknown" ]] && [[ $line == *".codec_type=\"video\""* ]]; then
    echo ParseFPS $line
    FPS=parse
  fi
  if [[ $FPS == "parse" ]] && [[ $line == *".r_frame_rate="* ]]; then
    echo ParseFPS $line
    FPS=${line##*=}
    FPS="${FPS%\"}"
    FPS="${FPS#\"}"
  fi
done <<< "$(ffprobe -v quiet -print_format flat -show_format -show_streams -i "$input")"
if [ "$FPS" == "unknown" ] || [ "$FPS" == "parse" ]; then 
  echo ParseFPS Unknown frame rate
fi
echo Found $FPS

Declare variable outside of the loop, set value and use it outside of loop requires done <<< "$(...)" syntax. Application need to be run within a context of current console. Quotes around the command keeps newlines of output stream.

Loop match for substrings then reads name=value pair, splits right-side part of last = character, drops first quote, drops last quote, we have a clean value to be used elsewhere.

Answer 4

Option 1a: While loop: Single line at a time: Input redirection

#!/bin/bash
filename='peptides.txt'
echo Start
while read p; do 
    echo $p
done < $filename

Option 1b: While loop: Single line at a time:
Open the file, read from a file descriptor (in this case file descriptor #4).

#!/bin/bash
filename='peptides.txt'
exec 4<$filename
echo Start
while read -u4 p ; do
    echo $p
done

Option 2: For loop: Read file into single variable and parse.
This syntax will parse "lines" based on any white space between the tokens. This still works because the given input file lines are single-word tokens. If there were more than one token per line, then this method would not work. Also, reading the full file into a single variable is not a good strategy for large files.

#!/bin/bash
filename='peptides.txt'
filelines=`cat $filename`
echo Start
for line in $filelines ; do
    echo $line
done

Answer 5

#!/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