2.8 Bonus: Loops

Teaching: 40 min || Exercises: 10 min

Overview

Questions:

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

Learning 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.
• Demonstrate how to see what commands have recently been executed.
• Re-run recently executed commands without retyping them.

Key Points:

• A for loop repeats commands once for everything 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.
• Use Ctrl-R to search through the previously entered commands.
• Use history to display recent commands, and !number to repeat a command by number.
• You can use the echo command to do a dry-run of the commands in the loop to check what they would do, but without actually running them.
• Two other commands that can be useful when looping through files are:
  • dirname to extract the directory name from a path.
  • basename to extract the file name from a path. Using basename <path> <suffix> will return the file name without the specified suffix (this is useful to extract the file name without the extension).

2.8.1 Background

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 02_unix_intro/creatures sub-directory which only has three example files, but the principles can be applied to 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.

2.8.2 The for loop

The general synthax for the for loop is:

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.

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 monotaur.dat and pipes the first two lines to the tail command, which then prints the second line of monotaur.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.

Same Symbols, Different Meanings

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.

Also note that loops can be used for other things than filenames, like a list of numbers or a subset of data.

Exercise 2.8.2.1: Write your own loop

How would you write a loop that echoes all 10 numbers from 0 to 9? Solution

Solution:

for loop_variable in 0 1 2 3 4 5 6 7 8 9
do
    echo $loop_variable
done

0
1
2
3
4
5
6
7
8
9

Exercise 2.8.2.2: Variables in Loops

This exercise refers to the 02_unix_intro/molecules sub-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

Exercise 2.8.2.3: Limiting Sets of Files

What would be the output of running the following loop in the 02_unix_intro/molecules sub-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 file name with zero or more characters before a letter c and zero or more characters after the letter c will be matched.

Exercise 2.8.2.4: Saving to a File in a Loop - Part One

In the 02_unix_intro/molecules sub-directory, what is the effect of this loop?

for alkanes in *.pdb
do
    echo $alkanes
    cat $alkanes > alkanes.pdb
done

1. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.
2. Prints cubane.pdb, ethane.pdb, and methane.pdb, and the text from all three files would be concatenated and saved to a file called alkanes.pdb.
3. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.
4. None of the above.

Solution:

1. The text from each file in turn gets written to the alkanes.pdb file. However, the file gets overwritten on each loop iteration, so the final content of alkanes.pdb is the text from the propane.pdb file.

Exercise 2.8.2.5: Saving to a File in a Loop - Part Two

Also in the 02_unix_intro/molecules sub-directory, what would be the output of the following loop?

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

1. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb would be concatenated and saved to a file called all.pdb.
2. The text from ethane.pdb will be saved to a file called all.pdb.
3. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be concatenated and saved to a file called all.pdb.
4. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be printed to the screen and saved to a file called all.pdb.

Solution:

3 is the correct answer. >> appends to a file, rather than overwriting it with the redirected output from a command. Given the output from the cat command has been redirected, nothing is printed to the screen.

Let’s continue with our example in the 02_unix_intro/creatures sub-directory. Here’s a slightly more complicated loop:

for filename in *.dat
do
    echo $filename
    head -n 100 $filename | tail -n 20
done

The shell starts by expanding *.dat to create the list of files it will process. The loop body then executes two commands for each of those files. The first command, echo, prints its command-line arguments to standard output. For example:

echo hello there

prints:

hello there

In this case, since the shell expands $filename to be the name of a file, echo $filename prints the name of the file. Note that we can’t write this as:

for filename in *.dat
do
    $filename
    head -n 100 $filename | tail -n 20
done

because then the first time through the loop, when $filename expanded to basilisk.dat, the shell would try to run basilisk.dat as a program. Finally, the head and tail combination selects lines 81-100 from whatever file is being processed (assuming the file has at least 100 lines).

Dealing with 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 this:

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:

Error

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
...

backing up files with cp

We would like to modify each of the files in 02_unix_intro/creatures, but also save a version of the original files, naming the copies original-basilisk.dat and original-unicorn.dat. We can’t use:

cp *.dat original-*.dat

because that would expand to:

cp basilisk.dat minotaur.dat unicorn.dat original-*.dat

This wouldn’t back up our files, instead we get an error:

Error

cp: target `original-*.dat' is not a directory

This problem arises when cp receives more than two inputs. When this happens, it expects the last input to be a directory where it can copy all the files it was passed. Since there is no directory named original-*.dat in the creatures directory we get an error.

Instead, we can use a loop:

for filename in *.dat
do
    cp $filename original-$filename
done

This loop runs the cp command once for each filename. The first time, when $filename expands to basilisk.dat, the shell executes:

cp basilisk.dat original-basilisk.dat

The second time, the command is:

cp minotaur.dat original-minotaur.dat

The third and last time, the command is:

cp unicorn.dat original-unicorn.dat

Since the cp command does not normally produce any output, it’s hard to check that the loop is doing the correct thing. However, we learned earlier how to print strings using echo, and we can modify the loop to use echo to print our commands without actually executing them. As such we can check what commands would be run in the unmodified loop.

The following diagram shows what happens when the modified loop is executed, and demonstrates how the judicious use of echo is a good debugging technique.

For Loop in Action

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 the up arrow. 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 up-arrow 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.

Those Who Know History Can Choose to Repeat It

Another way to repeat previous work is to use the history command to get a list of the last few hundred commands that have been executed, and then to use !123 (where ‘123’ is replaced by the command number) to repeat one of those commands. For example, if Nelle types this:

history | tail -n 5

  456  ls -l NENE0*.txt
  457  rm stats-NENE01729B.txt.txt
  458  bash goostats NENE01729B.txt stats-NENE01729B.txt
  459  ls -l NENE0*.txt
  460  history

then she can re-run goostats on NENE01729B.txt simply by typing !458.

:::::

Other History Commands

There are a number of other shortcut commands for getting at the history. - Ctrl-R enters a history search mode ‘reverse-i-search’ and finds the most recent command in your history that matches the text you enter next. Press Ctrl-R one or more additional times to search for earlier matches. - !! retrieves the immediately preceding command (you may or may not find this more convenient than using the up-arrow) - !$ retrieves the last word of the last command. That’s useful more often than you might expect: after bash goostats NENE01729B.txt stats-NENE01729B.txt, you can type less !$ to look at the file stats-NENE01729B.txt, which is quicker than doing up-arrow and editing the command-line.

Performing 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 file in *.pdb
do
  analyze $file > analyzed-$file
done

Exercise 2.8.2.6: Dry run with echo

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

# Version 1
for file in *.pdb
do
  echo analyze $file > analyzed-$file
done

# Version 2
for file in *.pdb
do
  echo "analyze $file > analyzed-$file"
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 redirects the output from the command echo analyze $file to a file, analyzed-$file. A series of files is generated: analyzed-cubane.pdb, analyzed-ethane.pdb etc.

Try both versions for yourself to see the output! Be sure to open the analyzed-*.pdb files to view their contents.

Nested loops

Exercise 2.8.2.7: Nested Loops

Suppose we want to set up 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!

Alternate solution

We can modify the code so that our command is quoted in an echo command: echo "mkdir $MOLECULE-$TEMP".
This would be the output:

mkdir cubane-25
mkdir cubane-30
mkdir cubane-37
mkdir cubane-40
mkdir ethane-25
mkdir ethane-30
mkdir ethane-37
mkdir ethane-40
mkdir methane-25
mkdir methane-30
mkdir methane-37
mkdir methane-40

Exercise 2.8.2.8: Creating a .csv Input File

This is an (optional) advanced exercise.

Let’s consider the files in the 02_unix_intro/sequencing directory (note: it’s not important if you don’t know what sequencing is!). This directory contains the results of an experiment where several samples were processed in two runs of the sequencing machine (run1/ and run2/). For each sample, there are two input files, which have suffix _1.fq.gz and _2.fq.gz.

The researcher analysing these files needs to produce a CSV file, which will be used as input to a pipeline, and the format of this file should be:

sample,input1,input2
sampleA,run1/sampleA_1.fq.gz,run1/sampleA_2.fq.gz
sampleB,run1/sampleB_1.fq.gz,run1/sampleB_2.fq.gz
sampleC,run1/sampleC_1.fq.gz,run1/sampleC_2.fq.gz
sampleD,run1/sampleD_1.fq.gz,run1/sampleD_2.fq.gz
sampleE,run2/sampleE_1.fq.gz,run2/sampleE_2.fq.gz
sampleF,run2/sampleF_1.fq.gz,run2/sampleF_2.fq.gz

Write a script that produces this file.

Hints - don’t hesitate to look at these tips, it’s a challenging exercise!. Don’t worry if you don’t understand anything, you will learn more about scripts in the next chapter

• Use a for loop to iterate through each sample (remember that each sample has two input files).
• You can combine multiple wildcards in a path, for example ls run*/*_1.fq.gz would list all files in folders starting with the word “run” and all files within those folders ending in “_1.fq.gz”.
• The command dirname can be used to extract the directory name from a path. For example: dirname run1/sampleA_1.fq.gz would return “run1” as the result.
• Conversely, the command basename can be used to extract the name of a file from a path. For example: basename run1/sampleA_1.fq.gz would return “sampleA_1.fq.gz”. Further, you can also remove a suffix at the end of the name by passing it as a second argument to basename: basename run1/sampleA_1.fq.gz _1.fq.gz would only return “sampleA”.
• You can store the result of a command in a variable with the syntax NAME=$(command). For example, DIR=$(dirname run1/sampleA_1.fq.gz) would create a variable called $DIR storing the result of the command, i.e. “run1”.

Solution:

Based on all the hints given, here is a script that would achieve the desired result:

#!/bin/bash

# first create a file with the CSV header (column names)
echo "sample,input1,input2" > samplesheet.csv

# for each file ending with `_1.fq.gz` (so we only process each sample once)
for FILE in run*/*_1.fq.gz
do
  # extract the directory name of the file
  DIR=$(dirname $FILE)

  # extract the prefix basename of the file
  BASE=$(basename $FILE _1.fq.gz)

  # append the name of the sample, and each input file path
  echo "${BASE},${DIR}/${BASE}_1.fq.gz,${DIR}/${BASE}_2.fq.gz" >> samplesheet.csv
done

This can be incredibly useful, especially for bioinformatic applications, when you may have to process hundreds of samples using standard pipelines. You will later find out the importance of this in module 07

2.8.3 Credit

Information on this page has been adapted and modified from the following source(s):

• Gabriel A. Devenyi (Ed.), Gerard Capes (Ed.), Colin Morris (Ed.), Will Pitchers (Ed.),Greg Wilson, Gerard Capes, Gabriel A. Devenyi, Christina Koch, Raniere Silva, Ashwin Srinath, … Vikram Chhatre. (2019, July). swcarpentry/shell-novice: Software Carpentry: the UNIX shell, June 2019 (Version v2019.06.1).

• https://github.com/cambiotraining/UnixIntro

• https://github.com/cambiotraining/unix-shell