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

---

One way to do it 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).

---

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

---

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 work tokens. If there were more than one token per line, then this method would not work as well. 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

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