Pipes and Filters

Overview

Teaching: 25 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 Linux’s ‘small pieces, loosely joined’ philosophy.

Go Wild, Count Characters and Words

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

output

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 list of all .pdb files in the current directory:

$ cd molecules
$ wc *.pdb

output

Wildcards

* is a wildcard. It matches zero or more characters, so *.pdb matches ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’ (including “.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’.

? is also a wildcard, but it only matches a single character. This means that p?.pdb would match pi.pdb or p5.pdb (if we had these two files in the molecules directory), 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 *.pdf. However, generally commands like wc and 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.

If we run wc -l instead of just wc, the output shows only the number of lines per file:

$ wc -l *.pdb

output

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:

Redirect Output

$ wc -l *.pdb > lengths.txt
$ cat 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.

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

output

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.

• Go forward one screenful by pressing the    SPACEBAR   .

• Go back one screenful by pressing B

• Go to the beginning of the file with G

• Go to the end of the file with SHIFT + G

• Press Q to quit.

Sort

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

output

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

output

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.

Redirecting to the same file

It’s a very bad idea to try redirecting the output of a command that operates on a file to the same file. For example:

$ sort -n lengths.txt > lengths.txt

Doing something like this may give you incorrect results and/or delete the contents of lengths.txt.

Pipe and Filter

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 can 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

output

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 for now.

We can chain pipes consecutively. For example, we can 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

output

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

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

output

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”). A third output channel called standard error (stderr) also exists. This channel is typically used for error or diagnostic messages, and it allows a user to pipe the output of one program into another while still receiving error messages in the terminal.

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.

This simple idea is why Linux have 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.

Nelle’s Pipeline: Checking Files

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 ~/PIL-data, Nelle types:

$ cd north-pacific-gyre/2012-07-03
$ wc -l *.txt

output

Now she types this:

$ wc -l *.txt | sort -n | head -n 5

output

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 -n 5

output

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

output

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.

Using Wildcards

When run in the molecules directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

1. ls *t*ane.pdb
2. ls *t?ne.*
3. ls *t??ne.pdb
4. ls ethane.*

Solution

3

What Does sort -n Do?

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

Explain why -n has this effect.

Solution

from the man page: -n, --numerical-sort: compare according to string numerical value.

By default, sort sorts its input lexicographically, treating each number as a string of characters and sorting them one character at a time. Lexicographically, 20 is greater than 19999999!

What Does < Mean?

What is the difference between:

$ wc -l < mydata.dat

and:

$ wc -l mydata.dat

Solution

In the first case, wc doesn’t have any command line parameters, so it reads from standard input, to which the shell directs the contents of ammonia.pdb. In the second case, wc gets a command line parameter telling it what file to open

What Does >> Mean?

What is the difference between:

$ echo hello > testfile01.txt

and:

$ echo hello >> testfile02.txt

Hint: Try executing each command twice in a row and then examining the output files.

Solution

>> appends to the redirected output, in this case the file testfile02.txt.

More on Wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

2015-10-23-calibration.txt
2015-10-23-dataset1.txt
2015-10-23-dataset2.txt
2015-10-23-dataset_overview.txt
2015-10-26-calibration.txt
2015-10-26-dataset1.txt
2015-10-26-dataset2.txt
2015-10-26-dataset_overview.txt
2015-11-23-calibration.txt
2015-11-23-dataset1.txt
2015-11-23-dataset2.txt
2015-11-23-dataset_overview.txt

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

$ cp *dataset* /backup/datasets
$ cp [blank]calibration[blank] /backup/calibration
$ cp 2015-[blank]-[blank] ~/send_to_bob/all_november_files/
$ cp [blank] ~/send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the [blank]s.

Solution

$ cp *calibration* /backup/calibration
$ cp 2015-11-* ~/send_to_bob/all_november_files/
$ cp 2015-??-23* ~/send_to_bob/all_datasets_created_on_a_23rd/

Piping Commands Together

In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work?

1. wc -l * > sort -n > head -n 3
2. wc -l * | sort -n | head -n 1-3
3. wc -l * | head -n 3 | sort -n
4. wc -l * | sort -n | head -n 3

Solution

4

Why Does uniq Only Remove Adjacent Duplicates?

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?

Solution

This way uniq only needs to keep track of the current line and the one immediately preceding it.

$ sort salmon.txt | uniq

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?

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

Solution

Pipe 1: all text Pipe 2:

2012-11-05,deer
2012-11-05,rabbit
2012-11-05,raccoon
2012-11-06,rabbit
2012-11-06,deer

Pipe 3:

2012-11-05,raccoon
2012-11-06,rabbit
2012-11-06,deer

Pipe 4:

2012-11-05,raccoon
2012-11-06,rabbit
2012-11-06,deer

final.txt:

2012-11-06,rabbit
2012-11-06,deer
2012-11-05,raccoon

Pipe Construction

For the file animals.txt from the previous exercise, the command:

$ 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)?

Solution

$ cut -d , -f 2 animals.txt | sort -u

or

$ cut -d , -f 2 animals.txt | sort | uniq

Removing Unneeded Files

Suppose you want to delete your processed data files, and only keep your raw files and processing script to save storage. The raw files end in .dat and the processed files end in .txt. Which of the following would remove all the processed data files, and only the processed data files?

1. rm ?.txt
2. rm *.txt
3. rm * .txt
4. rm *.*

Solution

2

Which Pipe?

A file called animals.txt contains 586 lines of data formatted as follows:

2012-11-05,deer
2012-11-05,rabbit
2012-11-05,raccoon
2012-11-06,rabbit
...

What command would you use to produce a table that shows the total count of each type of animal in the file?

1. sort animals.txt | uniq -c
2. sort -t, -k2,2 animals.txt | uniq -c
3. cut -d, -f 2 animals.txt | uniq -c
4. cut -d, -f 2 animals.txt | sort | uniq -c
5. cut -d, -f 2 animals.txt | sort | uniq -c | wc -l

Solution

4

Appending Data

Consider the file animals.txt, used in previous exercise. After these commands, select the alternative that corresponds the file animalsUpd.txt:

$ head -n 3 animals.txt > animalsUpd.txt
$ tail -n 2 animals.txt >> animalsUpd.txt

1. The first three lines of animals.txt
2. The last two lines of animals.txt
3. The first three lines and the last two lines of animals.txt
4. The second and third lines of animals.txt

Solution

3

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).