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 $p than just output to the screen.)
The environment variable SHELL is (from env):
SHELL=/bin/bash /bin/bash --version output:
GNU bash, version 3.1.17(1)-release (x86_64-suse-linux-gnu) Copyright (C) 2005 Free Software Foundation, Inc. cat /proc/version output:
Linux version 2.6.18.2-34-default (geeko@buildhost) (gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)) #1 SMP Mon Nov 27 11:46:27 UTC 2006 The file peptides.txt contains:
RKEKNVQ IPKKLLQK QYFHQLEKMNVK IPKKLLQK GDLSTALEVAIDCYEK QYFHQLEKMNVKIPENIYR RKEKNVQ VLAKHGKLQDAIN ILGFMK LEDVALQILL 16 Answers
One way to do it is:
while read p; do echo "$p" done <peptides.txt As pointed out in the comments, this has the side effects of trimming leading whitespace, interpreting backslash sequences, and skipping the last 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).
21cat peptides.txt | while read line do # do something with $line here done and the one-liner variant:
cat peptides.txt | while read line; do something_with_$line_here; done These options will skip the last line of the file if there is no trailing line feed.
You can avoid this by the following:
cat peptides.txt | while read line || [[ -n $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 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!
11A 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 "${my_array[@]}"; do # process the lines done More about the shell builtins
readandreadarraycommands - GNU- BashFAQ/001 - How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?
Related posts:
- Creating an array from a text file in Bash
- What is the difference between thee approaches to reading a file that has just one line?
- Bash while read loop extremely slow compared to cat, why?
Use a while loop, like this:
while IFS= read -r line; do echo "$line" done <file Notes:
If you don't set the
IFSproperly, you will lose indentation.
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:
- The blank line 4;
- Leading or trailing spaces on two lines;
- Maintaining the meaning of individual lines (i.e., each line is a record);
- 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 $line ]] in the while loop.)
More at the BASH FAQ
0If you don't want your read to be broken by newline character, use -
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "$line" done < "$1" Then run the script with file name as parameter.
This might be the simplest answer and maybe it don't work in all cases, but it is working great for me:
while read line;do echo "$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.
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
#!/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 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.
1@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 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 Another way to go about using xargs
<file_name | xargs -I {} echo {} echo can be replaced with other commands or piped further.
Answer: don't use bash for this task, use awk.
#! /usr/bin/env awk -f BEGIN { print("do anything you want here!"); } { print("processing line: ", $0); } END { print("and anything else here!"); And invoke with:
./awk-script.awk peptides.txt 
