Supplemental: Pipes and Filters

Overview

Teaching: 30 min
Exercises: 20 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. 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 list of all .pdb files in the current directory:

$ 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 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’.

? 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 an argument 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, and this is another example of orthogonal design.

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

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t, then a single character (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

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 ____calibration____ /backup/calibration
$ cp 2015-____-____ ~/send_to_bob/all_november_files/
$ cp ____ ~/send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

Solution

$ cp *calibration.txt /backup/calibration
$ cp 2015-11-* ~/send_to_bob/all_november_files/
$ cp *-23-dataset* ~send_to_bob/all_datasets_created_on_a_23rd/

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 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

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.

What Does sort -n Do?

If we run sort on a file containing the following lines:

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

The -n flag specifies a numeric sort, rather than alphabetical.

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 -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.

What Does >> Mean?

We have seen the use of >, but there is a similar operator >> which works slightly differently. By using the echo command to print strings, test the commands below to reveal the difference between the two operators:

$ 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

In the first example with >, the string “hello” is written to testfile01.txt, but the file gets overwritten each time we run the command.

We see from the second example that the >> operator also writes “hello” to a file (in this casetestfile02.txt), but appends the string to the file if it already exists (i.e. when we run it for the second time).

Appending Data

We have already met the head command, which prints lines from the start of a file. tail is similar, but prints lines from the end of a file instead.

Consider the file data-shell/data/animals.txt. After these commands, select the answer that corresponds to 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

Option 3 is correct. For option 1 to be correct we would only run the head command. For option 2 to be correct we would only run the tail command. For option 4 to be correct we would have to pipe the output of head into tail -2 by doing head -3 animals.txt | tail -2 >> animalsUpd.txt

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. 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.

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 of 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”.

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

Option 4 is the solution. The pipe character | is used to feed the standard output from one process to the standard input of another. > is used to redirect standard output to a file. Try it in the data-shell/molecules directory!

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”). A second 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 arguments, 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 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 ammonia.pdb, we could write wc < ammonia.pdb. In the first case, wc gets a command line argument telling it what file to open. In the second, wc doesn’t have any command line arguments, so it reads from standard input, but we have told the shell to send the contents of ammonia.pdb to wc’s standard input.

What Does < Mean?

Change directory to data-shell (the top level of our downloaded example data).

What is the difference between:

$ wc -l notes.txt

and:

$ wc -l < notes.txt

Solution

< is used to redirect input to a command.

In both examples, the shell returns the number of lines from the input to the wc command. In the first example, the input is the file notes.txt and the file name is given in the output from the wc command. In the second example, the contents of the file notes.txt are redirected to standard input. It is as if we have entered the contents of the file by typing at the prompt. Hence the file name is not given in the output - just the number of lines. Try this for yourself:

$ wc -l
this
is
a test
Ctrl-D # This lets the shell know you have finished typing the input

3

Why Does uniq Only Remove Adjacent Duplicates?

The command uniq removes adjacent duplicated lines from its input. For example, the file data-shell/data/salmon.txt contains:

coho
coho
steelhead
coho
steelhead
steelhead

Running the command uniq salmon.txt from the data-shell/data directory 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

$ sort salmon.txt | uniq

Pipe Reading Comprehension

A file called animals.txt (in the data-shell/data folder) 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

Hint: build the pipeline up one command at a time to test your understanding

Solution

The head command extracts the first 5 lines from animals.txt. Then, the last 3 lines are extracted from the previous 5 by using the tail command. With the sort -r command those 3 lines are sorted in reverse order and finally, the output is redirected to a file final.txt. The content of this file can be checked by executing cat final.txt. The file should contain the following lines:

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

uses the -d flag to separate each line by comma, and the -f flag to print the second field in each line, to give 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 | uniq

Which Pipe?

The file 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
...

Assuming your current directory is data-shell/data/, what command would you use to produce a table that shows the total count of each type of animal in the file?

1. grep {deer, rabbit, raccoon, deer, fox, bear} animals.txt | wc -l
2. sort animals.txt | uniq -c
3. sort -t, -k2,2 animals.txt | uniq -c
4. cut -d, -f 2 animals.txt | uniq -c
5. cut -d, -f 2 animals.txt | sort | uniq -c
6. cut -d, -f 2 animals.txt | sort | uniq -c | wc -l

Solution

Option 5. is the correct answer. If you have difficulty understanding why, try running the commands, or sub-sections of the pipelines (make sure you are in the data-shell/data directory).

Nelle’s Pipeline: Checking Files

Nelle has run her samples through the assay machines and created 17 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 18 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 -n 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 -n 5

 300 NENE02040B.txt
 300 NENE02040Z.txt
 300 NENE02043A.txt
 300 NENE02043B.txt
5040 total

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

NENE01971Z.txt    NENE02040Z.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.

Wildcard Expressions

Wildcard expressions can be very complex, but you can sometimes write them in ways that only use simple syntax, at the expense of being a bit more verbose.
Consider the directory data-shell/north-pacific-gyre/2012-07-03 : the wildcard expression *[AB].txt matches all files ending in A.txt or B.txt. Imagine you forgot about this.

1. Can you match the same set of files with basic wildcard expressions that do not use the [] syntax? Hint: You may need more than one expression.

2. The expression that you found and the expression from the lesson match the same set of files in this example. What is the small difference between the outputs?

3. Under what circumstances would your new expression produce an error message where the original one would not?

Solution

1. $ ls *A.txt
   $ ls *B.txt
   

2. The output from the new commands is separated because there are two commands.
3. When there are no files ending in A.txt, or there are no files ending in B.txt.

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

1. This would remove .txt files with one-character names
2. This is correct answer
3. The shell would expand * to match everything in the current directory, so the command would try to remove all matched files and an additional file called .txt
4. The shell would expand *.* to match all files with any extension, so this command would delete all files

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).