Loops

Overview

Teaching: 40 min
Exercises: 10 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.

• Trace the values taken on by a loop variable during execution of the loop.

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

• Explain why spaces and some punctuation characters shouldn’t be used in file names.

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).

loop syntax

This is what a for loop looks like in bash.

It starts with the keyword for. Next you choose a name for the loop variable. Here we use colors. then another keyword in and lastly a list of space delimited items to loop over.

Now the loop is setup and we’re ready to begin looping. The keyword do starts the loop. The line(s) between do and done will be run as many times as you have items. In our example code we have four colors so the loop will be run four times. the keyword done closes the loop.

So let’s try writing and running this loop:

for colors in brown blue yellow green
do
echo $colors
done

The do keyword marks the beginning of the loop.

With each iteration of the loop the value of the $colors variable is set to the next item from the list.

In the third line of our loop we’re using echo to output the current value of our $colors variable to the screen.

The done keyword signals the end of the loop and tells the shell to repeat the loop with the next item assigned to the $colors variable.

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 our four colors: brown, blue, yellow, and green. Each time the loop iterates, it will assign sucessive colors to the variable $colors.
The first time through the loop, $colors is brown. The interpreter runs the command echo $colors generating our first line of output. For the second iteration, $colors becomes blue. This time, the shell again runs echo $colors but the value of our $colors variable has now changed to “blue”.

The process is repeated for the third and fourth iteration of the loop. Since the list was only four items, the shell then exits the for loop.

Same Symbols, Different Meanings

Here we see > being used 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.

We have called the variable in this loop colors 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 brown blue yellow green
do
echo $x
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) increase the odds that the program won’t do what its readers think it does.

Variables in Loops

This exercise refers to the data-shell/molecules directory. ls gives the following output:

cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb

What is the output of the following code?

$ for datafile in *.pdb
> do
>    ls *.pdb
> done

Now, what is the output of the following code?

$ for datafile in *.pdb
> do
>	ls $datafile
> done

Why do these two loops give different outputs?

Solution

The first code block gives the same output on each iteration through the loop. Bash expands the wildcard *.pdb within the loop body (as well as before the loop starts) to match all files ending in .pdb and then lists them using ls. The expanded loop would look like this:

$ for datafile in cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> do
>	ls cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> done

cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb

The second code block lists a different file on each loop iteration. The value of the datafile variable is evaluated using $datafile, and then listed using ls.

cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb

Limiting Sets of Files

What would be the output of running the following loop in the data-shell/molecules directory?

$ for filename in c*
> do
>    ls $filename
> done

1. No files are listed.
2. All files are listed.
3. Only cubane.pdb, octane.pdb and pentane.pdb are listed.
4. Only cubane.pdb is listed.

Solution

4 is the correct answer. * matches zero or more characters, so any file name starting with the letter c, followed by zero or more other characters will be matched.

How would the output differ from using this command instead?

$ for filename in *c*
> do
>    ls $filename
> done

1. The same files would be listed.
2. All the files are listed this time.
3. No files are listed this time.
4. The files cubane.pdb and octane.pdb will be listed.
5. Only the file octane.pdb will be listed.

Solution

4 is the correct answer. * matches zero or more characters, so a file name with zero or more characters before a letter c and zero or more characters after the letter c will be matched.

Spaces in Names

Spaces are used to separate the elements of the list that we are going to loop over. If one of those elements contains a space character, we need to surround it with quotes, and do the same thing to our loop variable. Suppose our data files are named:

red dragon.dat
purple unicorn.dat

To loop over these files, we would need to add double quotes like so:

$ for filename in "red dragon.dat" "purple unicorn.dat"
> do
>     head -n 100 "$filename" | tail -n 20
> done

It is simpler to avoid using spaces (or other special characters) in filenames.

The files above don’t exist, so if we run the above code, the head command will be unable to find them, however the error message returned will show the name of the files it is expecting:

head: cannot open ‘red dragon.dat’ for reading: No such file or directory
head: cannot open ‘purple unicorn.dat’ for reading: No such file or directory

Try removing the quotes around $filename in the loop above to see the effect of the quote marks on spaces. Note that we get a result from the loop command for unicorn.dat when we run this code in the creatures directory:

head: cannot open ‘red’ for reading: No such file or directory
head: cannot open ‘dragon.dat’ for reading: No such file or directory
head: cannot open ‘purple’ for reading: No such file or directory
CGGTACCGAA
AAGGGTCGCG
CAAGTGTTCC

Nelle’s Pipeline: Processing Files

Nelle is now ready to process her data files using goostats — a shell script written by her supervisor. This calculates some statistics from a protein sample file, and takes two arguments:

1. an input file (containing the raw data)
2. an output file (to store the calculated statistics)

Since she’s still learning how to use the shell, she decides to build up the required commands in stages. Her first step is to make sure that she can select the right input files — remember, these are ones whose names end in ‘A’ or ‘B’, rather than ‘Z’. Starting from her home directory, Nelle types:

$ cd north-pacific-gyre/2012-07-03
$ for datafile in NENE*[AB].txt
> do
>     echo $datafile
> done

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...
NENE02043A.txt
NENE02043B.txt

Her next step is to decide what to call the files that the goostats analysis program will create. Prefixing each input file’s name with ‘stats’ seems simple, so she modifies her loop to do that:

$ for datafile in NENE*[AB].txt
> do
>     echo $datafile stats-$datafile
> done

NENE01729A.txt stats-NENE01729A.txt
NENE01729B.txt stats-NENE01729B.txt
NENE01736A.txt stats-NENE01736A.txt
...
NENE02043A.txt stats-NENE02043A.txt
NENE02043B.txt stats-NENE02043B.txt

She hasn’t actually run goostats yet, but now she’s sure she can select the right files and generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and Nelle is worried about making mistakes, so instead of re-entering her loop, she presses ↑. In response, the shell redisplays the whole loop on one line (using semi-colons to separate the pieces):

$ for datafile in NENE*[AB].txt; do echo $datafile stats-$datafile; done

Using the left arrow key, Nelle backs up and changes the command echo to bash goostats:

$ for datafile in NENE*[AB].txt; do bash goostats $datafile stats-$datafile; done

When she presses Enter, the shell runs the modified command. However, nothing appears to happen — there is no output. After a moment, Nelle realizes that since her script doesn’t print anything to the screen any longer, she has no idea whether it is running, much less how quickly. She kills the running command by typing Ctrl+C, uses ↑ to repeat the command, and edits it to read:

$ for datafile in NENE*[AB].txt; do echo $datafile; bash goostats $datafile stats-$datafile; done

Beginning and End

We can move to the beginning of a line in the shell by typing Ctrl+A and to the end using Ctrl+E.

When she runs her program now, it produces one line of output every five seconds or so:

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...

1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As a final check, she opens another terminal window, goes into north-pacific-gyre/2012-07-03, and uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so she decides to get some coffee and catch up on her reading.

When using variables it is also possible to put the names into curly braces to clearly delimit the variable name: $colors is equivalent to ${colors}. You may find this notation in other people’s programs.

Doing a Dry Run

A loop is a way to do many things at once — or to make many mistakes at once if it does the wrong thing. One way to check what a loop would do is to echo the commands it would run instead of actually running them.

Suppose we want to preview the commands the following loop will execute without actually running those commands:

$ for datafile in *.pdb
> do
>   cat $datafile >> all.pdb
> done

What is the difference between the two loops below, and which one would we want to run?

# Version 1
$ for datafile in *.pdb
> do
>   echo cat $datafile >> all.pdb
> done

# Version 2
$ for datafile in *.pdb
> do
>   echo "cat $datafile >> all.pdb"
> done

Solution

The second version is the one we want to run. This prints to screen everything enclosed in the quote marks, expanding the loop variable name because we have prefixed it with a dollar sign.

The first version appends the output from the command echo cat $datafile to the file, all.pdb. This file will just contain the list; cat cubane.pdb, cat ethane.pdb, cat methane.pdb etc.

Try both versions for yourself to see the output! Be sure to open the all.pdb file to view its contents.

Nested Loops

Suppose we want to set up a directory structure to organize some experiments measuring reaction rate constants with different compounds and different temperatures. What would be the result of the following code:

$ for species in cubane ethane methane
> do
>     for temperature in 25 30 37 40
>     do
>         mkdir $species-$temperature
>     done
> done

Solution

We have a nested loop, i.e. contained within another loop, so for each species in the outer loop, the inner loop (the nested loop) iterates over the list of temperatures, and creates a new directory for each combination.

Try running the code for yourself to see which directories are created!

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.

• Use the up-arrow key to scroll up through previous commands to edit and repeat them.