Finding Things

Objectives

• Use grep to select lines from text files that match simple patterns.
• Use find to find files whose names match simple patterns.
• Use the output of one command as the command-line parameters to another command.
• Explain what is meant by “text” and “binary” files, and why many common tools don’t handle the latter well.

That data I want is somewhere in here...

grep finds and prints lines in files that match a pattern. For our examples, we will use a file that contains three haikus taken from a 1998 competition in Salon magazine. For this set of examples we’re going to be working in the writing subdirectory:

$ cd
$ cd writing
$ cat haiku.txt

The Tao that is seen
Is not the true Tao, until
You bring fresh toner.

With searching comes loss
and the presence of absence:
"My Thesis" not found.

Yesterday it worked
Today it is not working
Software is like that.

Forever, or Five Years
^^^^^^^^^^^^^^^^^^^^^^

We haven't linked to the original haikus because they don't appear
to be on *Salon*'s site any longer. As `Jeff Rothenberg
said <http://www.clir.org/pubs/archives/ensuring.pdf>`__, "Digital
information lasts forever—or five years, whichever comes first."

Let’s find lines that contain the word “not”:

$ grep not haiku.txt

Is not the true Tao, until
"My Thesis" not found
Today it is not working

Here, not is the pattern we’re searching for. It’s pretty simple: every alphanumeric character matches against itself. After the pattern comes the name or names of the files we’re searching in. The output is the three lines in the file that contain the letters “not”.

Let’s try a different pattern: “day”.

$ grep day haiku.txt

Yesterday it worked
Today it is not working

This time, the output is lines containing the words “Yesterday” and “Today”, which both have the letters “day”. If we give grep the -w flag, it restricts matches to word boundaries, so that only lines with the word “day” will be printed:

$ grep -w day haiku.txt

In this case, there aren’t any, so grep‘s output is empty.

Another useful option is -n, which numbers the lines that match:

$ grep -n it haiku.txt

5:With searching comes loss
9:Yesterday it worked
10:Today it is not working

Here, we can see that lines 5, 9, and 10 contain the letters “it”.

We can combine flags as we do with other Unix commands. For example, since -i makes matching case-insensitive and -v inverts the match, using them both only prints lines that don’t match the pattern in any mix of upper and lower case:

$ grep -i -v the haiku.txt

You bring fresh toner.

With searching comes loss

Yesterday it worked
Today it is not working
Software is like that.

grep has lots of other options. To find out what they are, we can type man grep. man is the Unix “manual” command: it prints a description of a command and its options, and (if you’re lucky) provides a few examples of how to use it:

$ man grep

GREP(1)                                                                                              GREP(1)

NAME
grep, egrep, fgrep - print lines matching a pattern

SYNOPSIS
grep [OPTIONS] PATTERN [FILE...]
grep [OPTIONS] [-e PATTERN | -f FILE] [FILE...]

DESCRIPTION
grep  searches the named input FILEs (or standard input if no files are named, or if a single hyphen-
minus (-) is given as file name) for lines containing a match to the given PATTERN.  By default, grep
prints the matching lines.
...        ...        ...

OPTIONS
Generic Program Information
--help Print  a  usage  message  briefly summarizing these command-line options and the bug-reporting
address, then exit.

-V, --version
Print the version number of grep to the standard output stream.  This version number should be
included in all bug reports (see below).

Matcher Selection
-E, --extended-regexp
Interpret  PATTERN  as  an  extended regular expression (ERE, see below).  (-E is specified by
POSIX.)

-F, --fixed-strings
Interpret PATTERN as a list of fixed strings, separated by newlines, any of  which  is  to  be
matched.  (-F is specified by POSIX.)
...        ...        ...

Wildcards
^^^^^^^^^

``grep``'s real power doesn't come from its options, though; it
comes from the fact that patterns can include wildcards. (The
technical name for these is `regular
expressions <../../gloss.html#regular-expression>`__, which is what
the "re" in "grep" stands for.) Regular expressions are both complex
and powerful; if you want to do complex searches, please look at the
lesson on `our website <http://software-carpentry.org>`__. As a
taster, we can find lines that have an 'o' in the second position
like this:

::

    $ grep -E '^.o' haiku.txt
    You bring fresh toner.
    Today it is not working
    Software is like that.

We use the ``-E`` flag and put the pattern in quotes to prevent the
shell from trying to interpret it. (If the pattern contained a '\*',
for example, the shell would try to expand it before running
``grep``.) The '^' in the pattern anchors the match to the start of
the line. The '.' matches a single character (just like '?' in the
shell), while the 'o' matches an actual 'o'.

While grep finds lines in files, the find command finds files themselves. Again, it has a lot of options; to show how the simplest ones work, we’ll use the directory tree shown below.

Nelle’s writing directory contains one file called haiku.txt and four subdirectories: thesis (which is sadly empty), data (which contains two files one.txt and two.txt), a tools directory that contains the programs format and stats, and an empty subdirectory called old.

For our first command, let’s run find . -type d. As always, the . on its own means the current working directory, which is where we want our search to start; -type d means “things that are directories”. Sure enough, find‘s output is the names of the five directories in our little tree (including .):

$ find . -type d

./
./data
./thesis
./tools
./tools/old

If we change -type d to -type f, we get a listing of all the files instead:

$ find . -type f

./haiku.txt
./tools/stats
./tools/old/oldtool
./tools/format
./thesis/empty-draft.md
./data/one.txt
./data/two.txt

find automatically goes into subdirectories, their subdirectories, and so on to find everything that matches the pattern we’ve given it. If we don’t want it to, we can use -maxdepth to restrict the depth of search:

$ find . -maxdepth 1 -type f

./haiku.txt

The opposite of -maxdepth is -mindepth, which tells find to only report things that are at or below a certain depth. -mindepth 2 therefore finds all the files that are two or more levels below us:

$ find . -mindepth 2 -type f

./data/one.txt
./data/two.txt
./tools/format
./tools/stats

Now let’s try matching by name:

$ find . -name *.txt

./haiku.txt

We expected it to find all the text files, but it only prints out ./haiku.txt. The problem is that the shell expands wildcard characters like * before commands run. Since *.txt in the current directory expands to haiku.txt, the command we actually ran was:

$ find . -name haiku.txt

find did what we asked; we just asked for the wrong thing.

To get what we want, let’s do what we did with grep: put *.txt in single quotes to prevent the shell from expanding the * wildcard. This way, find actually gets the pattern *.txt, not the expanded filename haiku.txt:

$ find . -name '*.txt'

./data/one.txt
./data/two.txt
./haiku.txt

Listing vs. Finding
^^^^^^^^^^^^^^^^^^^

``ls`` and ``find`` can be made to do similar things given the right
options, but under normal circumstances, ``ls`` lists everything it
can, while ``find`` searches for things with certain properties and
shows them.

As we said earlier, the command line’s power lies in combining tools. We’ve seen how to do that with pipes; let’s look at another technique. As we just saw, find . -name '*.txt' gives us a list of all text files in or below the current directory. How can we combine that with wc -l to count the lines in all those files?

The simplest way is to put the find command inside $():

$ wc -l $(find . -name '*.txt')

11 ./haiku.txt
300 ./data/two.txt
70 ./data/one.txt
381 total

When the shell executes this command, the first thing it does is run whatever is inside the $(). It then replaces the $() expression with that command’s output. Since the output of find is the three filenames ./data/one.txt, ./data/two.txt, and ./haiku.txt, the shell constructs the command:

$ wc -l ./data/one.txt ./data/two.txt ./haiku.txt

which is what we wanted. This expansion is exactly what the shell does when it expands wildcards like * and ?, but lets us use any command we want as our own “wildcard”.

It’s very common to use find and grep together. The first finds files that match a pattern; the second looks for lines inside those files that match another pattern. Here, for example, we can find PDB files that contain iron atoms by looking for the string “FE” in all the .pdb files above the current directory:

$ grep FE $(find .. -name '*.pdb')

../data/pdb/heme.pdb:ATOM     25 FE           1      -0.924   0.535  -0.518

Binary Files
^^^^^^^^^^^^

We have focused exclusively on finding things in text files. What if
your data is stored as images, in databases, or in some other
format? One option would be to extend tools like ``grep`` to handle
those formats. This hasn't happened, and probably won't, because
there are too many formats to support.

The second option is to convert the data to text, or extract the
text-ish bits from the data. This is probably the most common
approach, since it only requires people to build one tool per data
format (to extract information). On the one hand, it makes simple
things easy to do. On the negative side, complex things are usually
impossible. For example, it's easy enough to write a program that
will extract X and Y dimensions from image files for ``grep`` to
play with, but how would you write something to find values in a
spreadsheet whose cells contained formulas?

The third choice is to recognize that the shell and text processing
have their limits, and to use a programming language such as Python
instead. When the time comes to do this, don't be too hard on the
shell: many modern programming languages, Python included, have
borrowed a lot of ideas from it, and imitation is also the sincerest
form of praise.

Conclusion

The Unix shell is older than most of the people who use it. It has survived so long because it is one of the most productive programming environments ever created—maybe even the most productive. Its syntax may be cryptic, but people who have mastered it can experiment with different commands interactively, then use what they have learned to automate their work. Graphical user interfaces may be better at the first, but the shell is still unbeaten at the second. And as Alfred North Whitehead wrote in 1911, “Civilization advances by extending the number of important operations which we can perform without thinking about them.”

Key Points

• Use find to find files and directories, and grep to find text patterns in files.
• $(command) inserts a command’s output in place.
• man command displays the manual page for a given command.

Write a short explanatory comment for the following shell script:

find . -name '*.dat' | wc -l | sort -n

The -v flag to grep inverts pattern matching, so that only lines which do not match the pattern are printed. Given that, which of the following commands will find all files in /data whose names end in ose.dat (e.g., sucrose.dat or maltose.dat), but do not contain the word temp?

1. find /data -name '*.dat' | grep ose | grep -v temp
2. find /data -name ose.dat | grep -v temp
3. grep -v temp $(find /data -name '*ose.dat')
4. None of the above.