Loops and Conditionals

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How can I perform the same actions on many different files?

Objectives

• Write a loop that applies one or more commands separately to each file in a set of files.

• Explain the difference between a variable’s name and its value.

Variables in Linux

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.

They are nothing to be concerned about, but are mainly used in for loops which we will cover below and bash scripting.

There are some variables that already exist in bash, like env, or HOME. Some need the $ sign before it (such as $HOME).

To access the contents of the variable HOME we can use echo.

$ echo $HOME

/Users/johnsmith

Loops

Loops are a programming construct which allow 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. They are 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 named basilisk.dat, minotaur.dat, and unicorn.dat. For this example, we’ll use the loops/ directory which only has three example files, but the principles can be applied to many many more files at once.

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

$ 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, but first let’s look at 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

and 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

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.

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.

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.

Conditionals

Conditional statements are also an option in bash, as well as functions. Although useful at times, we won’t be spending too much time on them here as they are best saved for programming itself.

The syntax for conditional statements in bash is as follows:

if [ condition ] ; then
  "do some stuff"
fi

Integer comparison	String Comparison	Meaning
-eq	= / ==	equal to
-ne	!=	not equal to
-lt / <	<	less than
-le / <=	<=	less than or equal to
-gt / >	>	greater than
-ge / >=	>=	greater than or equal to

Depending on whether you are dealing with a string or integer, the following comparison may be useful for you. ["$a" -lt "$b"] or (("$a" < "$b"))

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.