04-loop.md

layout	root	title
lesson	../..	Loops

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

Wildcards and tab completion are two ways to reduce typing (and typing mistakes). Another is to tell the shell to do something over and over again. Suppose we have several hundred genome data files named basilisk.dat, unicorn.dat, and so on. When new files arrive, we'd like to rename the existing ones to original-basilisk.dat and original-unicorn.dat. We can't use:

$ mv *.dat original-*.dat

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because that would expand (in the two-file case) to:

$ mv basilisk.dat unicorn.dat

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This wouldn't back up our files: it would replace the content of unicorn.dat with whatever's in basilisk.dat.

Instead, we can use a loop to do some operation once for each thing in a list. Here's a simple example that displays the first three lines of each file in turn:

$ for filename in basilisk.dat unicorn.dat
> do
>    head -3 $filename
> done

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COMMON NAME: basilisk
CLASSIFICATION: basiliscus vulgaris
UPDATED: 1745-05-02
COMMON NAME: unicorn
CLASSIFICATION: equus monoceros
UPDATED: 1738-11-24

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When the shell sees the keyword for, it knows it is supposed to repeat a command (or group of commands) once for each thing in a list. In this case, the list is the two filenames. Each time through the loop, the name of the thing currently being operated on is assigned to the variable called filename. Inside the loop, we get the variable's value by putting $ in front of it: $filename is basilisk.dat the first time through the loop, unicorn.dat the second, and so on. Finally, the command that's actually being run is our old friend head, so this loop prints out the first three lines of each data file in turn.

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.

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 -3 $x
done

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or:

for temperature in basilisk.dat unicorn.dat
do
    head -3 $temperature
done

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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.

Here's a slightly more complicated loop:

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

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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 parameters to standard output. For example:

$ echo hello there

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prints:

hello there

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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 -100 $filename | tail -20
done

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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.

Spaces in Names

Filename expansion in loops is another reason you should not use spaces in filenames. Suppose our data files are named:

basilisk.dat
red dragon.dat
unicorn.dat

If we try to process them using:

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

then the shell will expand *.dat to create:

basilisk.dat red dragon.dat unicorn.dat

With older versions of Bash, or most other shells, filename will then be assigned the following values in turn:

basilisk.dat
red
dragon.dat
unicorn.dat

That's a problem: head can't read files called red and dragon.dat because they don't exist, and won't be asked to read the file red dragon.dat.

We can make our script a little bit more robust by quoting our use of the variable:

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

but it's simpler just to avoid using spaces (or other special characters) in filenames.

Going back to our original file renaming problem, we can solve it using this loop:

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

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

mv basilisk.dat original-basilisk.dat

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The second time, the command is:

mv unicorn.dat original-unicorn.dat

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Measure Twice, Run Once

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. For example, we could write our file renaming loop like this:

for filename in *.dat
do
    echo mv $filename original-$filename
done

Instead of running mv, this loop runs echo, which prints out:

mv basilisk.dat original-basilisk.dat
mv unicorn.dat original-unicorn.dat

without actually running those commands. We can then use up-arrow to redisplay the loop, back-arrow to get to the word echo, delete it, and then press "enter" to run the loop with the actual mv commands. This isn't foolproof, but it's a handy way to see what's going to happen when you're still learning how loops work.

Nelle's Pipeline: Processing Files

Nelle is now ready to process her data files. 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 files—remember, these are ones whose names end in 'A' or 'B', rather than 'Z':

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

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

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

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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

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

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Using the left arrow key, Nelle backs up and changes the command echo to goostats ('bash' will be explained in next lesson):

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

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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 job by typing Control-C, uses up-arrow to repeat the command, and edits it to read:

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

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Beginning and End

We can move to the beginning of a line in the shell by typing ^A (which means Control-A) and to the end using ^E.

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

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

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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 -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.

Key Points

• A for loop repeats commands once for every thing in a list.
• Every for loop needs a variable to refer to the current "thing".
• Use $name to expand a variable (i.e., get its value).
• 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 history to display recent commands, and !number to repeat a command by number.

Challenges

1. Suppose that ls initially displays:

   fructose.dat    glucose.dat   sucrose.dat
   

   What is the output of:

   for datafile in *.dat
   do
       ls *.dat
   done
   

2. In the same directory, what is the effect of this loop?

   for sugar in *.dat
   do
       echo $sugar
       cat $sugar > xylose.dat
   done
   

   1. Prints fructose.dat, glucose.dat, and sucrose.dat, and copies sucrose.dat to create xylose.dat.
   2. Prints fructose.dat, glucose.dat, and sucrose.dat, and concatenates all three files to create xylose.dat.
   3. Prints fructose.dat, glucose.dat, sucrose.dat, and xylose.dat, and copies sucrose.dat to create xylose.dat.
   4. None of the above.

3. The expr does simple arithmetic using command-line parameters:

   $ expr 3 + 5
   8
   $ expr 30 / 5 - 2
   4
   

   Given this, what is the output of:

   for left in 2 3
   do
       for right in $left
       do
           expr $left + $right
       done
   done
   

4. Describe in words what the following loop does.

   for how in frog11 prcb redig
   do
       $how -limit 0.01 NENE01729B.txt
   done