Loops

Loops are a programming construct which allows us to repeat a command or set of commands for each item in a list. As such they are key to productivity improvements through automation. Similar to wildcards and tab completion, using loops also reduces the amount of typing required (and hence reduces the number of typing mistakes).

Suppose we have several hundred genome data files on which we have to perform the same operation. To illustrate how to automate operation on many files we will focus on the example stored in ~/unix_intro/exercises/creatures directory which only has three example files (basilisk.dat, minotaur.dat, and unicorn.dat), but the same principles can be applied to many many more files at once.

The structure of these files is the same: the common name, classification, and date of the update are presented on the first three lines, with DNA sequences on the following lines. Let's look at the files:

cd ~/unix_intro/exercises/creatures
head -n 5 basilisk.dat minotaur.dat unicorn.dat

We would like to print out the classification for each species, which is given on the second line of each file. For each file, we would need to execute the command head -n 2 and pipe this to tail -n 1. We'll use a loop to solve this problem.

Before we do it let's get familiar with the general form of a loop:

for thing in list_of_things
do
    operation_using $thing    # Indentation within the loop is not required, but aids legibility
done

Now we can apply this to our example like this:

for filename in basilisk.dat minotaur.dat unicorn.dat 
do 
    head -n 2 $filename | tail -n 1 
done

CLASSIFICATION: basiliscus vulgaris
CLASSIFICATION: bos hominus
CLASSIFICATION: equus monoceros

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 i.e:

for filename in basilisk.dat minotaur.dat unicorn.dat; do head -n 2 $filename | tail -n 1; done

When the shell sees the keyword for, it knows to repeat a command (or group of commands) once for each item in a list. Each time the loop runs (called an iteration), an item in the list is assigned in sequence to the variable, and the commands inside the loop are executed, before moving on to the next item 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 external command.

In this example, the list is three filenames: basilisk.dat, minotaur.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 pipes the first two lines to the tail command, which then prints the second line of basilisk.dat.

For the second iteration, $filename becomes minotaur.dat. This time, the shell runs head on minotaur.dat and pipes the first two lines to the tail command, which then prints the second line of minotaur.dat.

For the third iteration, $filename becomes unicorn.dat, so the shell runs the head command on that file, and tail on the output of that. Since the list was only three 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.

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 -n 2 $x | tail -n 1
done

or:

for temperature in basilisk.dat minotaur.dat unicorn.dat
do
    head -n 2 $temperature | tail -n 1
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.