6. Loops

Introducing 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. 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, unicorn.dat, and so on. For this example, we’ll use the creatures directory which only has two example files, but the principles can be applied to many many more files at once. We would like to print out the classification for each species, which is given on the second line of the 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

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

CLASSIFICATION: basiliscus vulgaris
CLASSIFICATION: equus monoceros

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 two filenames: basilisk.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 then prints the first three lines of basilisk.dat.

For the second iteration, $filename becomes unicorn.dat. This time, the shell runs head on unicorn.dat and prints the first three lines of unicorn.dat. Since the list was only two items, the shell exits the for loop.

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 unicorn.dat
 do
    head -n 2 $x | tail -n 1
 done

or:

$ for temperature in basilisk.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.

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

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

$ 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

Limiting Sets of Files

 $ for filename in c*
  do
     ls $filename
  done

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

</div>

Saving to a File in a Loop

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

NOTE: If you do NOT add ‘>’, then each $datafile will be overwritten as the next file in *.pdb is added to all.pdb. The finished all.pdb will only contain the contents of the last file in *.pdb.

Let’s continue with our example in the data-shell/creatures 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, echo, just prints its command-line arguments to standard output. For example:

$ echo hello there

hello there

In this case, since the shell expands $filename to be the name of a file, echo $filename just 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).

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 just 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

We would like to modify each of the files in data-shell/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 unicorn.dat original-*.dat

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

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

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.

 $ 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

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.

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

 $ for file in *.pdb
  do
    analyze $file  analyzed-$file
  done

  $ for file in *.pdb
   do
     echo "analyze $file  analyzed-$file"
   done

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