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

A few more things not covered by other answers:

Reading from a delimited file

# ':' is the delimiter here, and there are three fields on each line in the file
# IFS set below is restricted to the context of `read`, it doesn't affect any other code
while IFS=: read -r field1 field2 field3; do
  # process the fields
  # if the line has less than three fields, the missing fields will be set to an empty string
  # if the line has more than three fields, `field3` will get all the values, including the third field plus the delimiter(s)
done < input.txt

Reading from the output of another command, using process substitution

while read -r line; do
  # process the line
done < <(command ...)

This approach is better than command ... | while read -r line; do ... because the while loop here runs in the current shell rather than a subshell as in the case of the latter. See the related post A variable modified inside a while loop is not remembered.

Reading from a null delimited input, for example find ... -print0

while read -r -d '' line; do
  # logic
  # use a second 'read ... <<< "$line"' if we need to tokenize the line
done < <(find /path/to/dir -print0)

Related read: BashFAQ/020 - How can I find and safely handle file names containing newlines, spaces or both?

Reading from more than one file at a time

while read -u 3 -r line1 && read -u 4 -r line2; do
  # process the lines
  # note that the loop will end when we reach EOF on either of the files, because of the `&&`
done 3< input1.txt 4< input2.txt

Based on @chepner's answer here:

-u is a bash extension. For POSIX compatibility, each call would look something like read -r X <&3.

Reading a whole file into an array (Bash versions earlier to 4)

while read -r line; do
    my_array+=("$line")
done < my_file

If the file ends with an incomplete line (newline missing at the end), then:

while read -r line || [[ $line ]]; do
    my_array+=("$line")
done < my_file

Reading a whole file into an array (Bash versions 4x and later)

readarray -t my_array < my_file

or

mapfile -t my_array < my_file

And then

for line in "${my_array[@]}"; do
  # process the lines
done

• More about the shell builtins read and readarray commands - GNU

• More about IFS - Wikipedia

• BashFAQ/001 - How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?

Related posts:

• Creating an array from a text file in Bash
• What is the difference between thee approaches to reading a file that has just one line?
• Bash while read loop extremely slow compared to cat, why?

Answer 2

Use a while loop, like this:

while IFS= read -r line; do
   echo "$line"
done <file

Notes:

1. If you don't set the IFS properly, you will lose indentation.

2. You should almost always use the -r option with read.

3. Don't read lines with for

Answer 3

Suppose you have this file:

$ cat /tmp/test.txt
Line 1
    Line 2 has leading space
Line 3 followed by blank line

Line 5 (follows a blank line) and has trailing space    
Line 6 has no ending CR

There are four elements that will alter the meaning of the file output read by many Bash solutions:

1. The blank line 4;
2. Leading or trailing spaces on two lines;
3. Maintaining the meaning of individual lines (i.e., each line is a record);
4. The line 6 not terminated with a CR.

If you want the text file line by line including blank lines and terminating lines without CR, you must use a while loop and you must have an alternate test for the final line.

Here are the methods that may change the file (in comparison to what cat returns):

1) Lose the last line and leading and trailing spaces:

$ while read -r p; do printf "%s\n" "'$p'"; done </tmp/test.txt
'Line 1'
'Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space'

(If you do while IFS= read -r p; do printf "%s\n" "'$p'"; done </tmp/test.txt instead, you preserve the leading and trailing spaces but still lose the last line if it is not terminated with CR)

2) Using process substitution with cat will reads the entire file in one gulp and loses the meaning of individual lines:

$ for p in "$(cat /tmp/test.txt)"; do printf "%s\n" "'$p'"; done
'Line 1
    Line 2 has leading space
Line 3 followed by blank line

Line 5 (follows a blank line) and has trailing space    
Line 6 has no ending CR'

(If you remove the " from $(cat /tmp/test.txt) you read the file word by word rather than one gulp. Also probably not what is intended...)

---

The most robust and simplest way to read a file line-by-line and preserve all spacing is:

$ while IFS= read -r line || [[ -n $line ]]; do printf "'%s'\n" "$line"; done </tmp/test.txt
'Line 1'
'    Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space    '
'Line 6 has no ending CR'

If you want to strip leading and trading spaces, remove the IFS= part:

$ while read -r line || [[ -n $line ]]; do printf "'%s'\n" "$line"; done </tmp/test.txt
'Line 1'
'Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space'
'Line 6 has no ending CR'

(A text file without a terminating \n, while fairly common, is considered broken under POSIX. If you can count on the trailing \n you do not need || [[ -n $line ]] in the while loop.)

More at the BASH FAQ

Answer 4

This is no better than other answers, but is one more way to get the job done in a file without spaces (see comments). I find that I often need one-liners to dig through lists in text files without the extra step of using separate script files.

for word in $(cat peptides.txt); do echo $word; done

This format allows me to put it all in one command-line. Change the "echo $word" portion to whatever you want and you can issue multiple commands separated by semicolons. The following example uses the file's contents as arguments into two other scripts you may have written.

for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done

Or if you intend to use this like a stream editor (learn sed) you can dump the output to another file as follows.

for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done > outfile.txt

I've used these as written above because I have used text files where I've created them with one word per line. (See comments) If you have spaces that you don't want splitting your words/lines, it gets a little uglier, but the same command still works as follows:

OLDIFS=$IFS; IFS=$'\n'; for line in $(cat peptides.txt); do cmd_a.sh $line; cmd_b.py $line; done > outfile.txt; IFS=$OLDIFS

This just tells the shell to split on newlines only, not spaces, then returns the environment back to what it was previously. At this point, you may want to consider putting it all into a shell script rather than squeezing it all into a single line, though.

Best of luck!

Answer 5

One way to do it is:

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

As pointed out in the comments, this has the side effects of trimming leading whitespace, interpretting backslash sequences, and skipping the trailing line if it's missing a terminating linefeed. If these are concerns, you can do:

while IFS="" read -r p || [ -n "$p" ]
do
  printf '%s\n' "$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).

Answer 6

If you don't want your read to be broken by newline character, use -

#!/bin/bash
while IFS='' read -r line || [[ -n "$line" ]]; do
    echo "$line"
done < "$1"

Then run the script with file name as parameter.