5 Loops

Author

Hawlader Al-Mamun

5.1 What is loop?

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 exercise-data/creatures 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:

5.2 Understanding the Structure of a For-Loop in Bash


for thing in list_of_things 
  do 
    operation_using/command $thing 
  done

The word “for” indicates the start of a for-loop command:
```
for thing in list_of_things
```
This line initializes the loop, where thing is a variable that takes on the value of each item in list_of_things one at a time.
The word “do” indicates the start of the job execution list:
```
do
```
This marks the beginning of the commands to be executed for each item in the list.
Indentation within the loop is not required, but aids legibility:
```
    operation_using/command $thing
```
While not mandatory, indenting the commands inside the loop improves readability, making the script easier to understand and maintain.
The word “done” indicates the end of a loop:
```
done
```
This signifies the end of the loop, where the script will stop iterating over the list and move on to any commands following the loop.

We can apply this to our example like this:

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

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.

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, we first use echo to print the value that the variable $filename currently holds. This is not necessary for the result, but beneficial for us here to have an easier time to follow along. Next, we will run the head command on the file currently referred to by $filename. 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.

Note

Here we see > being used as 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 should redirect output or get the value of a variable.

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.

In the above examples, the variables (thing, filename, x and temperature) could have been given any other name, as long as it is meaningful to both the person writing the code and the person reading it.

5.3 Challange

Check the contents of the folder /mnt/s-ws/everyone/Halophila_ovalis/ using ls.

Print all the file names ends with fastq.
Print first 6 lines of each file.

Tip

echo $filename will print the file name
head -n 6 $filename will print first 6 lines from the file

Answer

for file in /mnt/s-ws/everyone/Halophila_ovalis/*.fastq
do
    echo $file
    head -n 6 $file
done