The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. I highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.
We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake: these are actually small programs.
Let's start by going back to molecules/ and creating a new file, middle.sh which will
become our shell script:
$ cd molecules
$ nano middle.sh
The command nano middle.sh opens the file middle.sh within the text editor "nano"
(which runs within the shell).
If the file does not exist, it will be created.
We can use the text editor to directly edit the file -- we'll simply insert the following line:
head -n 15 octane.pdb | tail -n 5
This is a variation on the pipe we constructed earlier:
it selects lines 11-15 of the file octane.pdb.
Remember, we are not running it as a command just yet:
we are putting the commands in a file.
Then we save the file (Ctrl-O in nano),
and exit the text editor (Ctrl-X in nano).
Check that the directory molecules now contains a file called middle.sh.
Once we have saved the file,
we can ask the shell to execute the commands it contains.
Our shell is called bash, so we run the following command:
$ bash middle.sh
ATOM 9 H 1 -4.502 0.681 0.785 1.00 0.00
ATOM 10 H 1 -5.254 -0.243 -0.537 1.00 0.00
ATOM 11 H 1 -4.357 1.252 -0.895 1.00 0.00
ATOM 12 H 1 -3.009 -0.741 -1.467 1.00 0.00
ATOM 13 H 1 -3.172 -1.337 0.206 1.00 0.00
Sure enough, our script's output is exactly what we would get if we ran that pipeline directly.
Text vs. Whatever
We usually call programs like Microsoft Word or LibreOffice Writer "text editors", but we need to be a bit more careful when it comes to programming. By default, Microsoft Word uses
.docxfiles to store not only text, but also formatting information about fonts, headings, and so on. This extra information isn't stored as characters, and doesn't mean anything to tools likehead: they expect input files to contain nothing but the letters, digits, and punctuation on a standard computer keyboard. When editing programs, therefore, you must either use a plain text editor, or be careful to save files as plain text.
What if we want to select lines from an arbitrary file?
We could edit middle.sh each time to change the filename,
but that would probably take longer than just retyping the command.
Instead, let's edit middle.sh and make it more versatile:
$ nano middle.sh
Now, within "nano", replace the text octane.pdb with the special variable called $1:
head -n 15 "$1" | tail -n 5
Inside a shell script,
$1 means "the first filename (or other parameter) on the command line".
We can now run our script like this:
$ bash middle.sh octane.pdb
ATOM 9 H 1 -4.502 0.681 0.785 1.00 0.00
ATOM 10 H 1 -5.254 -0.243 -0.537 1.00 0.00
ATOM 11 H 1 -4.357 1.252 -0.895 1.00 0.00
ATOM 12 H 1 -3.009 -0.741 -1.467 1.00 0.00
ATOM 13 H 1 -3.172 -1.337 0.206 1.00 0.00
or on a different file like this:
$ bash middle.sh pentane.pdb
ATOM 9 H 1 1.324 0.350 -1.332 1.00 0.00
ATOM 10 H 1 1.271 1.378 0.122 1.00 0.00
ATOM 11 H 1 -0.074 -0.384 1.288 1.00 0.00
ATOM 12 H 1 -0.048 -1.362 -0.205 1.00 0.00
ATOM 13 H 1 -1.183 0.500 -1.412 1.00 0.00
Double-Quotes Around Arguments
For the same reason that we put the loop variable inside double-quotes, in case the filename happens to contain any spaces, we surround
$1with double-quotes.
We still need to edit middle.sh each time we want to adjust the range of lines,
though.
Let's fix that by using the special variables $2 and $3 for the
number of lines to be passed to head and tail respectively:
$ nano middle.sh
head -n "$2" "$1" | tail -n "$3"
We can now run:
$ bash middle.sh pentane.pdb 15 5
ATOM 9 H 1 1.324 0.350 -1.332 1.00 0.00
ATOM 10 H 1 1.271 1.378 0.122 1.00 0.00
ATOM 11 H 1 -0.074 -0.384 1.288 1.00 0.00
ATOM 12 H 1 -0.048 -1.362 -0.205 1.00 0.00
ATOM 13 H 1 -1.183 0.500 -1.412 1.00 0.00
By changing the arguments to our command we can change our script's behaviour:
$ bash middle.sh pentane.pdb 20 5
ATOM 14 H 1 -1.259 1.420 0.112 1.00 0.00
ATOM 15 H 1 -2.608 -0.407 1.130 1.00 0.00
ATOM 16 H 1 -2.540 -1.303 -0.404 1.00 0.00
ATOM 17 H 1 -3.393 0.254 -0.321 1.00 0.00
TER 18 1
This works,
but it may take the next person who reads middle.sh a moment to figure out what it does.
We can improve our script by adding some comments at the top:
$ nano middle.sh
# Select lines from the middle of a file.
# Usage: bash middle.sh filename end_line num_lines
head -n "$2" "$1" | tail -n "$3"
A comment starts with a # character and runs to the end of the line.
The computer ignores comments,
but they're invaluable for helping people (including your future self) understand and use scripts.
The only caveat is that each time you modify the script,
you should check that the comment is still accurate:
an explanation that sends the reader in the wrong direction is worse than none at all.
What if we want to process many files in a single pipeline?
For example, if we want to sort our .pdb files by length, we would type:
$ wc -l *.pdb | sort -n
because wc -l lists the number of lines in the files
(recall that wc stands for 'word count', adding the -l flag means 'count lines' instead)
and sort -n sorts things numerically.
We could put this in a file,
but then it would only ever sort a list of .pdb files in the current directory.
If we want to be able to get a sorted list of other kinds of files,
we need a way to get all those names into the script.
We can't use $1, $2, and so on
because we don't know how many files there are.
Instead, we use the special variable $@,
which means,
"All of the command-line parameters to the shell script."
We also should put $@ inside double-quotes
to handle the case of parameters containing spaces
("$@" is equivalent to "$1" "$2" ...)
Here's an example:
$ nano sorted.sh
# Sort filenames by their length.
# Usage: bash sorted.sh one_or_more_filenames
wc -l "$@" | sort -n
$ bash sorted.sh *.pdb ../creatures/*.dat
9 methane.pdb
12 ethane.pdb
15 propane.pdb
20 cubane.pdb
21 pentane.pdb
30 octane.pdb
163 ../creatures/basilisk.dat
163 ../creatures/unicorn.dat
Suppose we have just run a series of commands that did something useful --- for example, that created a graph we'd like to use in a paper. We'd like to be able to re-create the graph later if we need to, so we want to save the commands in a file. Instead of typing them in again (and potentially getting them wrong) we can do this:
$ history | tail -n 5 > redo-figure-3.sh
The file redo-figure-3.sh now contains:
297 bash goostats -r NENE01729B.txt stats-NENE01729B.txt
298 bash goodiff stats-NENE01729B.txt /data/validated/01729.txt > 01729-differences.txt
299 cut -d ',' -f 2-3 01729-differences.txt > 01729-time-series.txt
300 ygraph --format scatter --color bw --borders none 01729-time-series.txt figure-3.png
301 history | tail -n 5 > redo-figure-3.sh
After a moment's work in an editor to remove the serial numbers on the commands,
and to remove the final line where we called the history command,
we have a completely accurate record of how we created that figure.
In practice, most people develop shell scripts by running commands at the shell prompt a few times
to make sure they're doing the right thing,
then saving them in a file for re-use.
This style of work allows people to recycle
what they discover about their data and their workflow with one call to history
and a bit of editing to clean up the output
and save it as a shell script.
Nelle's Pipeline: Creating a Script
An off-hand comment from her supervisor has made Nelle realize that
she should have provided a couple of extra parameters to goostats when she processed her files.
This might have been a disaster if she had done all the analysis by hand,
but thanks to for loops,
it will only take a couple of hours to re-do.
But experience has taught her that if something needs to be done twice, it will probably need to be done a third or fourth time as well. She runs the editor and writes the following:
# Calculate reduced stats for data files at J = 100 c/bp.
for datafile in "$@"
do
echo $datafile
bash goostats -J 100 -r $datafile stats-$datafile
done
(The parameters -J 100 and -r are the ones her supervisor said she should have used.)
She saves this in a file called do-stats.sh
so that she can now re-do the first stage of her analysis by typing:
$ bash do-stats.sh *[AB].txt
She can also do this:
$ bash do-stats.sh *[AB].txt | wc -l
so that the output is just the number of files processed rather than the names of the files that were processed.
One thing to note about Nelle's script is that it lets the person running it decide what files to process. She could have written it as:
# Calculate reduced stats for Site A and Site B data files at J = 100 c/bp.
for datafile in *[AB].txt
do
echo $datafile
bash goostats -J 100 -r $datafile stats-$datafile
done
The advantage is that this always selects the right files:
she doesn't have to remember to exclude the 'Z' files.
The disadvantage is that it always selects just those files --- she can't run it on all files
(including the 'Z' files),
or on the 'G' or 'H' files her colleagues in Antarctica are producing,
without editing the script.
If she wanted to be more adventurous,
she could modify her script to check for command-line parameters,
and use *[AB].txt if none were provided.
Of course, this introduces another tradeoff between flexibility and complexity.
Key Points:
- Save commands in files (usually called shell scripts) for re-use.
bash filenameruns the commands saved in a file.$@refers to all of a shell script's command-line parameters.$1,$2, etc., refer to the first command-line parameter, the second command-line parameter, etc.- Place variables in quotes if the values might have spaces in them.
- Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.