03-pipefilter.md

layout	title	subtitle	minutes
page	The Unix Shell	Pipes and Filters	15

Learning Objectives {.objectives}

• Redirect a command's output to a file. (Apply)
• Process a file instead of keyboard input using redirection. (Apply)
• Construct command pipelines with two or more stages. (Create)
• Explain what usually happens if a program or pipeline isn't given any input to process. (Understand)
• Explain Unix's "small pieces, loosely joined" philosophy. (Understand)

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 {.callout}

* 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 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. 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, and this is another example of orthogonal design.

Using wildcards {.challenge}

When run in the molecules directory, which ls command 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.*

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 {.callout}

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. 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 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 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 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 {.callout}

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 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 -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
5082 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.

What does sort -n do? {.challenge}

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.

What does < mean? {.challenge}

What is the difference between:

wc -l < mydata.dat

and:

wc -l mydata.dat

What does >> mean? {.challenge}

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.

More on bash wildcards {.challenge}

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.

Piping commands together {.challenge}

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

Why does uniq only remove adjacent duplicates? {.challenge}

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?

Pipe reading comprehension {.challenge}

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

Pipe Construction {.challenge}

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)?

Removing Unneeded Files {.challenge}

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 *.*

Wildcard Expressions {.challenge}

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. For example, 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?

Which Pipe? {.challenge}

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. 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