Pipes and Filters ***************** 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. Multi-step operations with bash ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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 complete list of ``.pdb`` files: :: $ 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 <../../gloss.html#wildcard>`__. It matches zero or more characters, so ``*.pdb`` matches ``ethane.pdb``, ``propane.pdb``, and so on. On the other hand, ``p*.pdb`` only matches ``pentane.pdb`` and ``propane.pdb``, because the 'p' at the front only matches itself. ``?`` 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. This means that commands like ``wc`` and ``ls`` never see the wildcard characters, just what those wildcards matched. This is another example of orthogonal design. 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 The ``>`` tells the shell to `redirect <../../gloss.html#redirect>`__ the command's output to a file instead of printing it to the screen. The shell will create the file if it doesn't exist, or overwrite the contents of that file if it does. (This is why there is no screen output: everything that ``wc`` would have printed has gone into the file ``lengths`` instead.) ``ls lengths`` confirms that the file exists: :: $ ls lengths :: lengths We can now send the content of ``lengths`` to the screen using ``cat lengths``. ``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 :: 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. 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 :: 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`` by putting ``> sorted-lengths`` after the command, just as we used ``> lengths`` to put the output of ``wc`` into ``lengths``. Once we've done that, we can run another command called ``head`` to get the first few lines in ``sorted-lengths``: :: $ sort -n lengths > sorted-lengths $ head -1 sorted-lengths :: 9 methane.pdb Using the parameter ``-1`` with ``head`` tells it that we only want the first line of the file; ``-20`` would get the first 20, and so on. Since ``sorted-lengths`` 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 | head -1 :: 9 methane.pdb The vertical bar between the two commands is called a `pipe <../../gloss.html#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. We can use another pipe to send the output of ``wc`` directly to ``sort``, which then sends its output to ``head``: :: $ wc -l *.pdb | sort -n | head -1 :: 9 methane.pdb This is exactly like a mathematician nesting functions like *sin(πx)2* and saying "the square of the sine of *x* times π". 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 <../../gloss.html#process>`__ in memory to hold the program's software and its current state. Every process has an input channel called `standard input <../../gloss.html#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 <../../gloss.html#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``. 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 -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 <../../gloss.html#pipe-and-filter>`__. We've already seen pipes; a `filter <../../gloss.html#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. Downlading data with redirection ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nelle is frustrated and decides to download some 16S sequences to pass the time. She can download a collection of datafiles automatically. There is a list of datasets in filesystem/data/metagenomics :: $ cd ~/Downloads/filesystem/data/metagenomics $ ls datasetlist.sh generate_download_commands.sh $ This command will download a dataset from the MG-RAST API and save it in sequences.fasta: :: $ curl http://api.metagenomics.anl.gov/download/mgm4522007.3?file=050.1 > EbM1.fasta If we examine this command line, we run the command "curl"; we give it a url with id numbers for the dataset we want, and the output of curl is redirected to the file EbM1.fasta. generate_download_commands.sh uses columns 1 and 2 of the data table to construct a list of commands like that above to download the data from MG-RAST. To automatically download the first five, we run generate_download_commands.sh and then run download-volta-data.sh: :: $ bash generate_download_commands.sh Generating download-volta-data.sh $ bash download-volta-data.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed .... 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, she 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 -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 -5 :: 300 NENE02040A.txt 300 NENE02040B.txt 300 NENE02040Z.txt 300 NENE02043A.txt 300 NENE02043B.txt 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. Key Points ^^^^^^^^^^ - ``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). Exercises ^^^^^^^^^ 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 is the difference between: :: wc -l < mydata.dat and: :: wc -l mydata.dat 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? 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 -5 | tail -3 | sort -r > final.txt 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)?