The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. I highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.

Loops are key to productivity improvements through automation as they allow us to execute commands repetitively. Similar to wildcards and tab completion, using loops also reduces the amount of typing (and typing mistakes). Suppose we have several hundred genome data files named basilisk.dat, unicorn.dat, and so on. In this example, we'll use the creatures directory which only has two example files, but the principles can be applied to many many more files at once. We would like to modify these files, but also save a version of the original files, naming the copies original-basilisk.dat and original-unicorn.dat. We can't use:

$ cp *.dat original-*.dat

because that would expand to:

$ cp basilisk.dat unicorn.dat original-*.dat

This wouldn't back up our files, instead we get an error:

cp: target 'original-*.dat' is not a directory

This problem arises when cp receives more than two inputs. When this happens, it expects the last input to be a directory where it can copy all the files it was passed. Since there is no directory named original-*.dat in the creatures directory we get an error.

Instead, we can use a loop to do some operation once for each thing in a list. Here's a simple example that displays the first three lines of each file in turn:

$ for filename in basilisk.dat unicorn.dat
> do
>    head -n 3 $filename
> done
COMMON NAME: basilisk
CLASSIFICATION: basiliscus vulgaris
UPDATED: 1745-05-02
COMMON NAME: unicorn
CLASSIFICATION: equus monoceros
UPDATED: 1738-11-24

When the shell sees the keyword for, it knows to repeat a command (or group of commands) once for each thing in a list. For each iteration, the name of the each thing is sequentially assigned to the variable and the commands inside the loop are executed before moving on to the next thing in the list. Inside the loop, we call for the variable's value by putting $ in front of it. The $ tells the shell interpreter to treat the variable as a variable name and substitute its value in its place, rather than treat it as text or an external command.

In this example, the list is two filenames: basilisk.dat and unicorn.dat. Each time the loop iterates, it will assign a file name to the variable filename and run the head command. The first time through the loop, $filename is basilisk.dat. The interpreter runs the command head on basilisk.dat, and the prints the first three lines of basilisk.dat. For the second iteration, $filename becomes unicorn.dat. This time, the shell runs head on unicorn.dat and prints the first three lines of unicorn.dat. Since the list was only two items, the shell exits the for loop.

When using variables it is also possible to put the names into curly braces to clearly delimit the variable name: $filename is equivalent to ${filename}, but is different from ${file}name. You may find this notation in other people's programs.

Follow the Prompt

The shell prompt changes from $ to > and back again as we were typing in our loop. The second prompt, >, is different to remind us that we haven't finished typing a complete command yet. A semicolon, ;, can be used to separate two commands written on a single line.

Same Symbols, Different Meanings

Here we see > being used a shell prompt, whereas > is also used to redirect output. Similarly, $ is used as a shell prompt, but, as we saw earlier, it is also used to ask the shell to get the value of a variable.

If the shell prints > or $ then it expects you to type something, and the symbol is a prompt.

If you type > or $ yourself, it is an instruction from you that the shell to redirect output or get the value of a variable.

We have called the variable in this loop filename in order to make its purpose clearer to human readers. The shell itself doesn't care what the variable is called; if we wrote this loop as:

for x in basilisk.dat unicorn.dat
    head -n 3 $x


for temperature in basilisk.dat unicorn.dat
    head -n 3 $temperature

it would work exactly the same way. Don't do this. Programs are only useful if people can understand them, so meaningless names (like x) or misleading names (like temperature) increase the odds that the program won't do what its readers think it does.

Here's a slightly more complicated loop:

for filename in *.dat
    echo $filename
    head -n 100 $filename | tail -n 20

The shell starts by expanding *.dat to create the list of files it will process. The loop body then executes two commands for each of those files. The first, echo, just prints its command-line parameters to standard output. For example:

$ echo hello there


hello there

In this case, since the shell expands $filename to be the name of a file, echo $filename just prints the name of the file. Note that we can't write this as:

for filename in *.dat
    head -n 100 $filename | tail -n 20

because then the first time through the loop, when $filename expanded to basilisk.dat, the shell would try to run basilisk.dat as a program. Finally, the head and tail combination selects lines 81-100 from whatever file is being processed (assuming the file has at least 100 lines).

Spaces in Names

Whitespace is used to separate the elements on the list that we are going to loop over. If on the list we have elements with whitespace we need to quote those elements and our variable when using it. Suppose our data files are named:

red dragon.dat purple unicorn.dat

We need to use

for filename in "red dragon.dat" "purple unicorn.dat" do head -n 100 "$filename" | tail -n 20 done

It is simpler just to avoid using whitespaces (or other special characters) in filenames.

The files above don't exist, so if we run the above code, the head command will be unable to find them, however the error message returned will show the name of the files it is expecting: head: cannot open ‘red dragon.dat’ for reading: No such file or directory head: cannot open ‘purple unicorn.dat’ for reading: No such file or directory

Try removing the quotes around $filename in the loop above to see the effect of the quote marks on whitespace: head: cannot open ‘red’ for reading: No such file or directory head: cannot open ‘dragon.dat’ for reading: No such file or directory head: cannot open ‘purple’ for reading: No such file or directory head: cannot open ‘unicorn.dat’ for reading: No such file or directory

Going back to our original file copying problem, we can solve it using this loop:

for filename in *.dat
    cp $filename original-$filename

This loop runs the cp command once for each filename. The first time, when $filename expands to basilisk.dat, the shell executes:

cp basilisk.dat original-basilisk.dat

The second time, the command is:

cp unicorn.dat original-unicorn.dat

Since the cp command does not normally produce any output, it's hard to check that the loop is doing the correct thing. By prefixing the command with echo it is possible to see each command as it would be executed.

Nelle's Pipeline: Processing Files

Nelle is now ready to process her data files. Since she's still learning how to use the shell, she decides to build up the required commands in stages. Her first step is to make sure that she can select the right files --- remember, these are ones whose names end in 'A' or 'B', rather than 'Z'. Starting from her home directory, Nelle types:

$ cd north-pacific-gyre/2012-07-03
$ for datafile in *[AB].txt
> do
>     echo $datafile
> done

Her next step is to decide what to call the files that the goostats analysis program will create. Prefixing each input file's name with "stats" seems simple, so she modifies her loop to do that:

$ for datafile in *[AB].txt
> do
>     echo $datafile stats-$datafile
> done
NENE01729A.txt stats-NENE01729A.txt
NENE01729B.txt stats-NENE01729B.txt
NENE01736A.txt stats-NENE01736A.txt
NENE02043A.txt stats-NENE02043A.txt
NENE02043B.txt stats-NENE02043B.txt

She hasn't actually run goostats yet, but now she's sure she can select the right files and generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and Nelle is worried about making mistakes, so instead of re-entering her loop, she presses the up arrow. In response, the shell redisplays the whole loop on one line (using semi-colons to separate the pieces):

$ for datafile in *[AB].txt; do echo $datafile stats-$datafile; done

Using the left arrow key, Nelle backs up and changes the command echo to bash goostats:

$ for datafile in *[AB].txt; do bash goostats $datafile stats-$datafile; done

When she presses Enter, the shell runs the modified command. However, nothing appears to happen --- there is no output. After a moment, Nelle realizes that since her script doesn't print anything to the screen any longer, she has no idea whether it is running, much less how quickly. She kills the running command by typing Ctrl-C, uses up-arrow to repeat the command, and edits it to read:

$ for datafile in *[AB].txt; do echo $datafile; bash goostats $datafile stats-$datafile; done

Beginning and End

We can move to the beginning of a line in the shell by typing Ctrl-A and to the end using Ctrl-E.

When she runs her program now, it produces one line of output every five seconds or so:


1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As a final check, she opens another terminal window, goes into north-pacific-gyre/2012-07-03, and uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so she decides to get some coffee and catch up on her reading.

Those Who Know History Can Choose to Repeat It

Another way to repeat previous work is to use the history command to get a list of the last few hundred commands that have been executed, and then to use !123 (where "123" is replaced by the command number) to repeat one of those commands. For example, if Nelle types this:

 $ history | tail -n 5
   456  ls -l NENE0*.txt
   457  rm stats-NENE01729B.txt.txt
   458  bash goostats NENE01729B.txt stats-NENE01729B.txt
   459  ls -l NENE0*.txt
   460  history

then she can re-run goostats on NENE01729B.txt simply by typing !458.

## Other History Commands

There are a number of other shortcut commands for getting at the history.

  • Ctrl-R enters a history search mode "reverse-i-search" and finds the most recent command in your history that matches the text you enter next. Press Ctrl-R one or more additional times to search for earlier matches.
  • !! retrieves the immediately preceding command (you may or may not find this more convenient than using the up-arrow)
  • !$ retrieves the last word of the last command. That's useful more often than you might expect: after bash goostats NENE01729B.txt stats-NENE01729B.txt, you can type less !$ to look at the file stats-NENE01729B.txt, which is quicker than doing up-arrow and editing the command-line.

Key Points:

  • A for loop repeats commands once for every thing in a list.
  • Every for loop needs a variable to refer to the thing it is currently operating on.
  • Use $name to expand a variable (i.e., get its value). ${name} can also be used.
  • Do not use spaces, quotes, or wildcard characters such as '*' or '?' in filenames, as it complicates variable expansion.
  • Give files consistent names that are easy to match with wildcard patterns to make it easy to select them for looping.
  • Use the up-arrow key to scroll up through previous commands to edit and repeat them.
  • Use Ctrl-R to search through the previously entered commands.
  • Use history to display recent commands, and !number to repeat a command by number.


Part 6: Shell Scripts