Lesson 4: Intro to Loops - joslynnlee/CHEM-454 GitHub Wiki
Lesson adapted from ""The Carpentries""
Introduction
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. 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 creatures directory which only has three example files, but the principles can be applied to many many more files at once.
Change into the creatures directory:
cd creatures
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 one file:
cat unicorn.dat
This has the common name, classification, date and DNA sequences. Let's see if the other two have similar heading. Use head to view the first 5 lines:
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
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.
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 should redirect output or get the value of a variable.
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 an 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.
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 X.