- Redirect a command's output to a file.
- Process a file instead of keyboard input using redirection.
- Construct command pipelines with two or more stages.
- Explain what usually happens if a program or pipeline isn't given any input to process.
- Explain Unix's "small pieces, loosely joined" philosophy.
Now that we know a few basic commands, we can finally look at the shell's most powerful feature: the ease with which it lets us combine existing programs in new ways. We'll start with a directory called
molecules that contains six files describing some simple organic molecules. The
.pdb extension indicates that these files are in Protein Data Bank format, a simple text format that specifies the type and position of each atom in the molecule.
$ ls molecules
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
Let's go into that directory with
cd and run the command
wc is the "word count" command: it counts the number of lines, words, and characters in files. The
*.pdb matches zero or more characters, so the shell turns
*.pdb into a complete list of
$ cd molecules $ wc *.pdb
20 156 1158 cubane.pdb 12 84 622 ethane.pdb 9 57 422 methane.pdb 30 246 1828 octane.pdb 21 165 1226 pentane.pdb 15 111 825 propane.pdb 107 819 6081 total
* is a wildcard. It matches zero or more characters, so
propane.pdb, and so on. On the other hand,
p*.pdb only matches
propane.pdb, because the 'p' at the front only matches itself.
? is also a wildcard, but it only matches a single character. This means that
p5.pdb, but not
propane.pdb. We can use any number of wildcards at a time: for example,
p*.p?* matches anything that starts with a 'p' and ends with '.', 'p', and at least one more character (since the '?' has to match one character, and the final '*' can match any number of characters). Thus,
p*.p?* would match
preferred.practice, and even
p.pi (since the first '*' can match no characters at all), but not
quality.practice (doesn't start with 'p') or
preferred.p (there isn't at least one character after the '.p').
When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the command that was asked for. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as a parameter to the command as it is. For example typing
ls *.pdf in the molecules directory (which contains only files with names ending with
.pdb) results in an error message that there is no file called
ls see the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that deals with expanding wildcards, and this another example of orthogonal design.
If we run
wc -l instead of just
wc, the output shows only the number of lines per file:
$ wc -l *.pdb
20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total
We can also use
-w to get only the number of words, or
-c to get only the number of characters.
Which of these files is shortest? It's an easy question to answer when there are only six files, but what if there were 6000? Our first step toward a solution is to run the command:
$ wc -l *.pdb > lengths.txt
The greater than symbol,
>, tells the shell to redirect the command's output to a file instead of printing it to the screen. The shell will create the file if it doesn't exist, or overwrite the contents of that file if it does. (This is why there is no screen output: everything that
wc would have printed has gone into the file
ls lengths.txt confirms that the file exists:
$ ls lengths.txt
We can now send the content of
lengths.txt to the screen using
cat stands for "concatenate": it prints the contents of files one after another. There's only one file in this case, so
cat just shows us what it contains:
$ cat lengths.txt
20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total
Now let's use the
sort command to sort its contents. We will also use the -n flag to specify that the sort is numerical instead of alphabetical. This does not change the file; instead, it sends the sorted result to the screen:
$ sort -n lengths.txt
9 methane.pdb 12 ethane.pdb 15 propane.pdb 20 cubane.pdb 21 pentane.pdb 30 octane.pdb 107 total
We can put the sorted list of lines in another temporary file called
sorted-lengths.txt by putting
> sorted-lengths.txt after the command, just as we used
> lengths.txt to put the output of
lengths.txt. Once we've done that, we can run another command called
head to get the first few lines in
$ sort -n lengths.txt > sorted-lengths.txt $ head -1 sorted-lengths.txt
Using the parameter
head tells it that we only want the first line of the file;
-20 would get the first 20, and so on. Since
sorted-lengths.txt contains the lengths of our files ordered from least to greatest, the output of
head must be the file with the fewest lines.
If you think this is confusing, you're in good company: even once you understand what
head do, all those intermediate files make it hard to follow what's going on. We can make it easier to understand by running
$ sort -n lengths.txt | head -1
The vertical bar between the two commands is called a pipe. It tells the shell that we want to use the output of the command on the left as the input to the command on the right. The computer might create a temporary file if it needs to, or copy data from one program to the other in memory, or something else entirely; we don't have to know or care.
We can use another pipe to send the output of
wc directly to
sort, which then sends its output to
$ wc -l *.pdb | sort -n | head -1
This is exactly like a mathematician nesting functions like log(3x) and saying "the log of three times x". In our case, the calculation is "head of sort of line count of
Here's what actually happens behind the scenes when we create a pipe. When a computer runs a program --- any program --- it creates a process in memory to hold the program's software and its current state. Every process has an input channel called standard input. (By this point, you may be surprised that the name is so memorable, but don't worry: most Unix programmers call it "stdin". Every process also has a default output channel called standard output (or "stdout").
The shell is actually just another program. Under normal circumstances, whatever we type on the keyboard is sent to the shell on its standard input, and whatever it produces on standard output is displayed on our screen. When we tell the shell to run a program, it creates a new process and temporarily sends whatever we type on our keyboard to that process's standard input, and whatever the process sends to standard output to the screen.
Here's what happens when we run
wc -l *.pdb > lengths.txt. The shell starts by telling the computer to create a new process to run the
wc program. Since we've provided some filenames as parameters,
wc reads from them instead of from standard input. And since we've used
> to redirect output to a file, the shell connects the process's standard output to that file.
If we run
wc -l *.pdb | sort -n instead, the shell creates two processes (one for each process in the pipe) so that
sort run simultaneously. The standard output of
wc is fed directly to the standard input of
sort; since there's no redirection with
sort's output goes to the screen. And if we run
wc -l *.pdb | sort -n | head -1, we get three processes with data flowing from the files, through
sort, and from
head to the screen.
This simple idea is why Unix has been so successful. Instead of creating enormous programs that try to do many different things, Unix programmers focus on creating lots of simple tools that each do one job well, and that work well with each other. This programming model is called "pipes and filters". We've already seen pipes; a filter is a program like
sort that transforms a stream of input into a stream of output. Almost all of the standard Unix tools can work this way: unless told to do otherwise, they read from standard input, do something with what they've read, and write to standard output.
The key is that any program that reads lines of text from standard input and writes lines of text to standard output can be combined with every other program that behaves this way as well. You can and should write your programs this way so that you and other people can put those programs into pipes to multiply their power.
As well as using
> to redirect a program's output, we can use
< to redirect its input, i.e., to read from a file instead of from standard input. For example, instead of writing
wc ammonia.pdb, we could write
wc < ammonia.pdb. In the first case,
wc gets a command line parameter telling it what file to open. In the second,
wc doesn't have any command line parameters, so it reads from standard input, but we have told the shell to send the contents of
wc's standard input.
Nelle has run her samples through the assay machines and created 1520 files in the
north-pacific-gyre/2012-07-03 directory described earlier. As a quick sanity check, starting from her home directory, Nelle types:
$ cd north-pacific-gyre/2012-07-03 $ wc -l *.txt
The output is 1520 lines that look like this:
300 NENE01729A.txt 300 NENE01729B.txt 300 NENE01736A.txt 300 NENE01751A.txt 300 NENE01751B.txt 300 NENE01812A.txt ... ...
Now she types this:
$ wc -l *.txt | sort -n | head -5
240 NENE02018B.txt 300 NENE01729A.txt 300 NENE01729B.txt 300 NENE01736A.txt 300 NENE01751A.txt
Whoops: one of the files is 60 lines shorter than the others. When she goes back and checks it, she sees that she did that assay at 8:00 on a Monday morning --- someone was probably in using the machine on the weekend, and she forgot to reset it. Before re-running that sample, she checks to see if any files have too much data:
$ wc -l *.txt | sort -n | tail -5
300 NENE02040A.txt 300 NENE02040B.txt 300 NENE02040Z.txt 300 NENE02043A.txt 300 NENE02043B.txt
Those numbers look good --- but what's that 'Z' doing there in the third-to-last line? All of her samples should be marked 'A' or 'B'; by convention, her lab uses 'Z' to indicate samples with missing information. To find others like it, she does this:
$ ls *Z.txt
Sure enough, when she checks the log on her laptop, there's no depth recorded for either of those samples. Since it's too late to get the information any other way, she must exclude those two files from her analysis. She could just delete them using
rm, but there are actually some analyses she might do later where depth doesn't matter, so instead, she'll just be careful later on to select files using the wildcard expression
*[AB].txt. As always, the '*' matches any number of characters; the expression
[AB] matches either an 'A' or a 'B', so this matches all the valid data files she has.
If we run
sort on this file:
10 2 19 22 6
the output is:
10 19 2 22 6
If we run
sort -n on the same input, we get this instead:
2 6 10 19 22
-n has this effect.
What is the difference between:
echo hello > testfile01.txt
echo hello >> testfile02.txt
Hint: Try executing each command twice in a row and then examining the output files.
In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work?
wc -l * > sort -n > head -3
wc -l * | sort -n | head 1-3
wc -l * | head -3 | sort -n
wc -l * | sort -n | head -3
The command `uniq` removes adjacent duplicated lines from its input. For example, if a file `salmon.txt` contains:
coho coho steelhead coho steelhead steelhead
then `uniq salmon.txt` produces:
coho steelhead coho steelhead
Why do you think `uniq` only removes *adjacent* duplicated lines? (Hint: think about very large data sets.) What other command could you combine with it in a pipe to remove all duplicated lines?
A file called
animals.txt contains the following data:
2012-11-05,deer 2012-11-05,rabbit 2012-11-05,raccoon 2012-11-06,rabbit 2012-11-06,deer 2012-11-06,fox 2012-11-07,rabbit 2012-11-07,bear
What text passes through each of the pipes and the final redirect in the pipeline below?
cat animals.txt | head -5 | tail -3 | sort -r > final.txt
$ cut -d , -f 2 animals.txt
produces the following output:
deer rabbit raccoon rabbit deer fox rabbit bear
What other command(s) could be added to this in a pipeline to find out what animals the file contains (without any duplicates in their names)?
sort -nsorts items numerically instead of lexically. Without
-nnumerical items will be sorted by the first digit, and then the second digit, and so on.
>first deletes the contents of the file if it exists.
>>appends output to the end of the file.
sort salmon.txt | uniq
2012-11-06,rabbit 2012-11-06,deer 2012-11-05,raccoon
cut -d , -f 2 animals.txt | sort | uniq