Intro to Unix, Part 7: Finding Things

The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. I highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.

In the same way that many of us now use "Google" as a verb meaning "to find", Unix programmers often use the word "grep". "grep" is a contraction of "global/regular expression/print", a common sequence of operations in early Unix text editors. It is also the name of a very useful command-line program.

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.

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. The grep command searches through the file, looking for matches to the pattern specified. To use it type grep, then the pattern we're searching for and finally the name of the file (or 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: "The".

$ grep The haiku.txt

The Tao that is seen
"My Thesis" not found.

This time, two lines that include the letters "The" are outputted. However, one instance of those letters is contained within a larger word, "Thesis".

To restrict matches to lines containing the word "The" on its own, we can give grep with the -w flag. This will limit matches to word boundaries.

$ grep -w The haiku.txt

The Tao that is seen

Note that a "word boundary" includes the start and end of a line, so not just letters surrounded by spaces. Sometimes we don't want to search for a single word, but a phrase. This is also easy to do with grep by putting the phrase in quotes.

$ grep -w "is not" haiku.txt

Today it is not working

We've now seen that you don't have to have quotes around single words, but it is useful to use quotes when searching for multiple words. It also helps to make it easier to distinguish between the search term or phrase and the file being searched. We will use quotes in the remaining examples.

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 options (i.e. flags) as we do with other Unix commands. For example, let's find the lines that contain the word "the". We can combine the option -w to find the lines that contain the word "the" and -n to number the lines that match:

$ grep -n -w "the" haiku.txt

2:Is not the true Tao, until
6:and the presence of absence:

Now we want to use the option -i to make our search case-insensitive:

$ grep -n -w -i "the" haiku.txt

1:The Tao that is seen
2:Is not the true Tao, until
6:and the presence of absence:

Now, we want to use the option -v to invert our search, i.e., we want to output the lines that do not contain the word "the".

$ grep -n -w -v "the" haiku.txt

1:The Tao that is seen
3:You bring fresh toner.
4:
5:With searching comes loss
7:"My Thesis" not found.
8:
9:Yesterday it worked
10:Today it is not working
11:Software is like that.

grep has lots of other options. To find out what they are, we can type:

$ grep --help

Usage: grep [OPTION]... PATTERN [FILE]...
Search for PATTERN in each FILE or standard input.
PATTERN is, by default, a basic regular expression (BRE).
Example: grep -i 'hello world' menu.h main.c

Regexp selection and interpretation:
  -E, --extended-regexp     PATTERN is an extended regular expression (ERE)
  -F, --fixed-strings       PATTERN is a set of newline-separated fixed strings
  -G, --basic-regexp        PATTERN is a basic regular expression (BRE)
  -P, --perl-regexp         PATTERN is a Perl regular expression
  -e, --regexp=PATTERN      use PATTERN for matching
  -f, --file=FILE           obtain PATTERN from FILE
  -i, --ignore-case         ignore case distinctions
  -w, --word-regexp         force PATTERN to match only whole words
  -x, --line-regexp         force PATTERN to match only whole lines
  -z, --null-data           a data line ends in 0 byte, not newline

Miscellaneous:
...        ...        ...

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, 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. 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.

Nelle's writing directory contains one file called haiku.txt and four subdirectories: thesis (which contains a sadly empty file, empty-draft.md), data (which contains two files one.txt and two.txt), a tools directory that contains the programs format and stats, and a subdirectory called old, with a file oldtool.

For our first command, let's run find ..

$ find .

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

As always, the . on its own means the current working directory, which is where we want our search to start. find's output is the names of every file and directory under the current working directory. This can seem useless at first but find has many options to filter the output and in this lesson we will discover some of them.

The first option in our list is -type d that means "things that are directories". Sure enough, find's output is the names of the six directories in our little tree (including .):

$ find . -type d

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

Notice that the objects find finds are not listed in any particular order. 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

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

Key Points

  • find finds files with specific properties that match patterns.
  • grep selects lines in files that match patterns.
  • --help is a flag supported by many bash commands, and programs that can be run from within Bash, to display more information on how to use these commands or programs.
  • man command displays the manual page for a given command.
  • $(command) inserts a command's output in place.