5 Ch. 1.5: Pipes and Filters

Which of these files contains the fewest lines?  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:

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. The cat command gets its name from ‘concatenate’ i.e. join together, and 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

Now let’s use the sort command to sort its contents.

10
2
19
22
6

10
19
2
22
6

2
6
10
19
22

We will also use the -n option to specify that the sort is numerical instead of alphanumerical. 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.

$ sort -n lengths.txt > lengths.txt

$ echo The echo command prints text

The echo command prints text

$ echo hello > testfile01.txt

$ echo hello >> testfile02.txt

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

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, he calculation is ‘head of sort of line count of *.pdb’.

The redirection and pipes used in the last few commands are illustrated below:

This idea of linking programs together 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 sortthat 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.

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

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

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

$ cut -d , -f 2 animals.txt

deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear

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

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

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 delete them using rm, but there are actually some analyses she might do later where depth doesn’t matter, so instead, she’ll have to 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.