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

User · Answer

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  lt    TOTAL LINES  i         do       LINE  head -n i  USER FILE   tail -n1        echo  LINE    done

User · Answer

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  lt    1    Then run the script with file name as parameter

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cat 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

User · Answer

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  gt  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  gt  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

User · Answer

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 · Answer

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

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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 · Answer

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      amp  amp      line       codec type   video         then     echo ParseFPS  line     FPS parse   fi   if     FPS     parse      amp  amp      line       r frame rate        then     echo ParseFPS  line     FPS   line          FPS    FPS          FPS    FPS        fi done  lt  lt  lt     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  lt  lt  lt           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

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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  lt   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 lt  filename echo Start while read -u4 p   do     echo  p done

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Use a while loop  like this   while IFS  read -r line  do    echo   line  done  lt file   Notes     If you don t set the IFS properly  you will lose indentation  You should almost always use the -r option with read  Don t read lines with for

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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  quot  line quot  done lt peptides txt  if you need to enclose in parenthesis for spaces  while read line do echo   quot  line  quot  done lt peptides txt  Ahhh this is pretty much the same as the answer that got upvoted most  but its all on one line

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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  lt  input txt   Reading from the output of another command  using process substitution  while read -r line  do     process the line done  lt   lt  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      lt  lt  lt    line   if we need to tokenize the line done  lt   lt  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  amp  amp  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   amp  amp   done 3 lt  input1 txt 4 lt  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  lt  amp 3   Reading a whole file into an array  Bash versions earlier to 4   while read -r line  do     my array     line   done  lt  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  lt  my file   Reading a whole file into an array  Bash versions 4x and later   readarray -t my array  lt  my file   or  mapfile -t my array  lt  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

User · Answer

One way to do it is   while read p  do   echo   p  done  lt 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  lt  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 lt peptides txt   Here  10 is just an arbitrary number  different from 0  1  2

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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  lt  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  lt  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  lt  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  lt  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

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