The Unix Shell

Loops

Wildcards and tab completion are two ways to reduce typing (and typing mistakes). Another is to tell the shell to do something over and over again. Suppose we have several hundred genome data files named basilisk.dat, minotaur.dat, unicorn.dat, and so on. In this example, we’ll use the test_directory/creatures directory which only has three 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 and rename them as original-basilisk.dat, original-minotaur.dat, original-unicorn.dat. We can’t use:

$ mv *.dat original-*.dat

because that would expand to:

$ mv basilisk.dat minotaur.dat unicorn.dat original-*.dat

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

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

This a problem arises when mv receives more than two inputs. When this happens, it expects the last input to be a directory where it can move 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 minotaur.dat unicorn.dat
> do
>    head -3 $filename
> done

COMMON NAME: basilisk
CLASSIFICATION: basiliscus vulgaris
UPDATED: 1745-05-02
COMMON NAME: minotaur
CLASSIFICATION: minotaurus maximus
UPDATED: 1764-09-12
COMMON NAME: unicorn
CLASSIFICATION: equus monoceros
UPDATED: 1738-11-24

When the shell sees the keyword for, it knows it is supposed to repeat a command (or group of commands) once for each thing in a list. In this case, the list is the three filenames. Each time through the loop, the name of the thing currently being operated on is assigned to the variable called filename. Inside the loop, we get the variable’s value by putting $ in front of it: $filename is basilisk.dat the first time through the loop, minotaur.dat the second, unicorn.dat the third, and so on.

By using the dollar sign we are telling the shell interpreter to treat filename as a variable name and substitute its value on its place, but not as some text or external command. 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.

Finally, the command that’s actually being run is our old friend head, so this loop prints out the first three lines of each data file in turn.

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 minotaur.dat unicorn.dat
do
    head -3 $x
done

or:

for temperature in basilisk.dat minotaur.dat unicorn.dat
do
    head -3 $temperature
done

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
do
    echo $filename
    head -100 $filename | tail -20
done

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

prints:

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
do
    $filename
    head -100 $filename | tail -20
done

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.

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

for filename in *.dat
do
    mv $filename original-$filename
done

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

mv basilisk.dat original-basilisk.dat

The second time, the command is:

mv minotaur.dat original-minotaur.dat

The third time, the command is:

mv unicorn.dat original-unicorn.dat

fructose.dat    glucose.dat   sucrose.dat

for datafile in *.dat
do
    ls *.dat
done

for datafile in *.dat
do
  ls $datafile
done

for sugar in *.dat
do
    echo $sugar
    cat $sugar > xylose.dat
done

fructose.dat    glucose.dat   sucrose.dat   maltose.txt

for datafile in *.dat
do
    cat $datafile >> sugar.dat
done

for file in *.dat
do
  analyze $file > analyzed-$file
done

# Version 1
for file in *.dat
do
  echo analyze $file > analyzed-$file
done

# Version 2
for file in *.dat
do
  echo "analyze $file > analyzed-$file"
done

$ expr 3 + 5
8
$ expr 30 / 5 - 2
4

for left in 2 3
do
    for right in $left
    do
        expr $left + $right
    done
done