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
unicorn.dat, and so on. In 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.
When new files arrive,
we’d like to rename the existing ones to
We can’t use:
$ mv *.dat original-*.dat
because that would expand (in the two-file case) to:
$ mv basilisk.dat unicorn.dat
This wouldn’t back up our files:
it would replace the content of
unicorn.dat with whatever’s in
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
COMMON NAME: basilisk CLASSIFICATION: basiliscus vulgaris UPDATED: 1745-05-02 COMMON NAME: unicorn CLASSIFICATION: equus monoceros UPDATED: 1738-11-24
When the shell sees the keyword
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
Inside the loop,
we get the variable’s value by putting
$ in front of it:
basilisk.dat the first time through the loop,
unicorn.dat the second,
and so on.
the command that’s actually being run is our old friend
so this loop prints out the first three lines of each data file in turn.
Follow the Prompt
The shell prompt changes from
>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
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
for temperature in basilisk.dat unicorn.dat do head -3 $temperature 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
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
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.
echo, just prints its command-line parameters to standard output.
$ echo 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 -100 $filename | tail -20 done
because then the first time through the loop,
$filename expanded to
basilisk.dat, the shell would try to run
basilisk.dat as a program.
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 $filename | tail -20 done
then the shell will expand
basilisk.dat red dragon.dat unicorn.dat
With older versions of Bash, or most other shells,
filenamewill then be assigned the following values in turn:
basilisk.dat red dragon.dat unicorn.dat
That’s a problem:
headcan’t read files called
dragon.datbecause they don’t exist, and won’t be asked to read the file
We can make our script a little bit more robust by quoting our use of the variable:
for filename in *.dat do head -100 "$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
This loop runs the
mv command once for each filename.
The first time,
$filename expands to
the shell executes:
mv basilisk.dat original-basilisk.dat
The second time, the command is:
mv unicorn.dat original-unicorn.dat
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
mvcommands. 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 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
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 *[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
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
Using the left arrow key,
Nelle backs up and changes the command
$ for datafile in *[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 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
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
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,
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
historycommand 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
NENE01729B.txtsimply by typing
forloop repeats commands once for every thing in a list.
forloop needs a variable to refer to the current “thing”.
$nameto expand a variable (i.e., get its value).
historyto display recent commands, and
!numberto repeat a command by number.
ls initially displays:
fructose.dat glucose.dat sucrose.dat
What is the output of:
for datafile in *.dat do ls *.dat done
In the same directory, what is the effect of this loop?
for sugar in *.dat do echo $sugar cat $sugar > xylose.dat done
sucrose.dat, and copies
sucrose.dat, and concatenates all three files to create
xylose.dat, and copies
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
Describe in words what the following loop does.
for how in frog11 prcb redig do $how -limit 0.01 NENE01729B.txt done