Pipes and Filters

Overview

Teaching: 15 min
Exercises: 0 min
Questions
  • How can I combine existing commands to do new things?

Objectives
  • 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.

For training purposes, let’s use some data from the Software Carpentry workshop. We will download them using the GitHub interface and the git clone command. Let’s put them inside the linux_workshop folder.

$ cd ~/linux_workshop
$ git clone https://github.com/silshack/pipes.git

This will create a folder called pipes, which will contain a subfolder called molecules. Lets’s see its contents.

$ cd pipes
$ cd molecules
$ ls
cubane.pdb    ethane.pdb    methane.pdb
octane.pdb    pentane.pdb   propane.pdb

The folder molecules 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.

We can print out the contents of these files using the cat command. Let’s print out methane.pdb:

$ cat methane.pdb
COMPND      METHANE
AUTHOR      DAVE WOODCOCK  95 12 18
ATOM      1  C           1       0.257  -0.363   0.000  1.00  0.00
ATOM      2  H           1       0.257   0.727   0.000  1.00  0.00
ATOM      3  H           1       0.771  -0.727   0.890  1.00  0.00
ATOM      4  H           1       0.771  -0.727  -0.890  1.00  0.00
ATOM      5  H           1      -0.771  -0.727   0.000  1.00  0.00
TER       6              1
END

Now, I would like to introduce you to a command that could be very useful: wc, which stands for “word count” and counts the number of lines, words, and characters in files. Let’s apply it to methane.pdb and see what we get:

$ wc methane.pdb
  9  57 422 methane.pdb

So, the file methane.pdb has 9 lines, 57 words, and 422 characters. Now, let’s apply the wc command to all six files that have the .pdb extension. We can run wc command six times, but thankfully, there is a way to do it with a single use of the wc command using the very useful feature of Linux called wildcards. Let me show you how it works:

$ 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 every file that ends with ‘.pdb’. On the other hand, p*.pdb only matches pentane.pdb and propane.pdb, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’. If you want to apply the command to all the files in the folder, you can do wc *.

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. (This is why there is no screen output: everything that wc would have printed has gone into the file lengths.txt instead.) The shell will create the file if it doesn’t exist. If the file exists, it will be silently overwritten, which may lead to data loss and thus requires some caution. ls lengths.txt confirms that the file exists:

$ ls lengths.txt
lengths.txt

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

$ cat lengths.txt
  20  cubane.pdb
  12  ethane.pdb
   9  methane.pdb
  30  octane.pdb
  21  pentane.pdb
  15  propane.pdb
 107  total

Output Page by Page

We’ll continue to use cat in this lesson, for convenience and consistency, but it has the disadvantage that it always dumps the whole file onto your screen. More useful in practice is the command less, which you use with $ less lengths.txt. This displays a screenful of the file, and then stops. You can go forward one screenful by pressing the spacebar, or back one by pressing b. Press q to quit.

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 wc into lengths.txt. Once we’ve done that, we can run another command called head to get the first few lines in sorted-lengths.txt:

$ sort -n lengths.txt > sorted-lengths.txt
$ head -n 1 sorted-lengths.txt
  9  methane.pdb

Using the parameter -n 1 with head tells it that we only want the first line of the file; -n 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 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.txt | head -n 1
  9  methane.pdb

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.

Nothing prevents us from chaining pipes consecutively. That is, we can for example send the output of wc directly to sort, and then the resulting output to head. Thus we first use a pipe to send the output of wc to sort:

$ wc -l *.pdb | sort -n
   9 methane.pdb
  12 ethane.pdb
  15 propane.pdb
  20 cubane.pdb
  21 pentane.pdb
  30 octane.pdb
 107 total

And now we send the output ot this pipe, through another pipe, to head, so that the full pipeline becomes:

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

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 *.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 Linux 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 wc and 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 -n 1, we get three processes with data flowing from the files, through wc to sort, and from sort through head to the screen.

Redirects and Pipes

This simple idea is why Linux has been so successful. Instead of creating enormous programs that try to do many different things, Linux 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 Linux 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 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 ammonia.pdb to wc’s standard input.

Pipe Reading Comprehension

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? Note that sort -r sorts in reverse order.

$ cat animals.txt | head -n 5 | tail -n 3 | sort -r > final.txt

Key Points

  • cat displays the contents of its inputs.

  • head displays the first few lines of its input.

  • tail displays the last few lines of its input.

  • sort sorts its inputs.

  • wc counts lines, words, and characters in its inputs.

  • * matches zero or more characters in a filename, so *.txt matches all files ending in .txt.

  • ? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.

  • 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).