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• 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 *.pdb. wc is the “word count” command: it counts the number of lines, words, and characters in files. The * in *.pdb matches zero or more characters, so the shell turns *.pdb into a complete list of .pdb files:

  $ 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

Wildcards

* is a wildcard. It matches zero or more
characters, so *.pdb matches ethane.pdb, propane.pdb, and so on.
On the other hand, p*.pdb only matches pentane.pdb and
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 p?.pdb matches pi.pdb or 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. This means that commands like wc and ls never see
the wildcard characters, just what those wildcards matched. This is
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
  

The > 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 lengths instead.) ls lengths confirms that the file exists:

  $ ls lengths 
  
  lengths
  

We can now send the content of lengths to the screen using cat lengths. 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

   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
  
    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 by putting > sorted-lengths after the command, just as we used > lengths to put the output of wc into lengths. Once we've done that, we can run another command called head to get the first few lines in sorted-lengths:

  $ sort -n lengths > sorted-lengths
  $ head -1 sorted-lengths

  9  methane.pdb
  

Using the parameter -1 with 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 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 wc, sort, and 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 and head together:

  $ sort -n lengths | head -1

  9  methane.pdb
  

The vertical bar between the two commands is called a [pipe](../../gloss.html#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 head:

  $ wc -l *.pdb | sort -n | head -1

  9  methane.pdb

This is exactly like a mathematician nesting functions like $sin(\pi \cdot x)^{2}$ and saying “the square of the sine of $x$ times $\pi$”. In our case, the calculation is “head of sort of line count of *.pdb”.

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. 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 wc and sort start 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 wc to sort, and from sort through 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 wc or 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.

Redirecting Input

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 cubane.pdb, we could write
wc < cubane.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 cubane.pdb to wc's
standard input.

• command > file redirects a command's output to a file.
• first | second is a pipeline: the output of the first command is used as the input to the second.
• The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).