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The Unix Shell, Intermediate

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Regular Expressions

Overview

Teaching: 25 min
Exercises: 20 min
Questions

  • What are regular expressions?

Objectives

  • Use grep to select lines from text files that match simple patterns.

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.

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, “Digital information lasts forever — or five years, whichever comes first.” Luckily, popular content often has backups.

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, please visit the manual.

Using grep

Which command would result in the following output:

and the presence of absence:
  1. grep "of" haiku.txt
  2. grep -E "of" haiku.txt
  3. grep -w "of" haiku.txt
  4. grep -i "of" haiku.txt

Solution

The correct answer is 3, because the -w flag looks only for whole-word matches. The other options will all match “of” when part of another word.

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 Expression Libraries

All the popular programming languages has at least one regular expression library. Not always they have the same default behaviour so you need to be careful.

The regular expressions that we saw so far didn’t make use of any operators or metacharacters. The characters that are operators are

The power of regular expression is more visible in structured data.

head snap.txt

Mass	x	y	z	vx	vy	vz
M_sol	Parsecs	Parsecs	Parsecs	km/s	km/s	km/s

0.11	1.15	0.6	1.3	-0.01	0.89	1.12
0.13	-0.87	0.25	-1.11	0.24	0.98	1.23
0.22	1.18	-0.38	0.7	-0.01	1.04	1.08
0.16	1.17	-0.37	0.72	0.13	0.96	0.97
0.15	0.22	-0.7	-0.35	-0.25	0.29	0.84
0.34	0.9	0.65	1.73	0.13	1.95	0.42
0.27	-0.04	0.01	0.07	-0.05	1.16	0.69

If we want to find particles with mass of 0.13, we can’t use

grep 0.13 snap.txt

0.13	-0.87	0.25	-1.11	0.24	0.98	1.23
0.16	1.17	-0.37	0.72	0.13	0.96	0.97
0.34	0.9	0.65	1.73	0.13	1.95	0.42
0.47	0.39	-0.54	-0.7	-0.13	0.93	1.16
0.3	0.17	-0.69	-0.37	0.13	0.45	0.78
0.37	-0.13	-0.03	0.08	0.77	0.65	1.57
0.13	0.0	-0.1	-0.32	-0.49	0.46	1.16
0.13	1.09	-0.66	0.41	0.21	0.24	0.02
0.13	1.16	0.45	1.37	0.3	0.08	0.87
0.13	0.72	-0.36	0.9	0.34	0.59	0.94
0.13	0.21	-0.53	-0.74	0.12	0.61	1.38
0.13	-1.19	-0.05	-0.82	0.73	0.32	1.36
0.16	0.81	0.13	0.81	0.25	0.09	1.01
0.13	-0.03	-0.22	-1.32	0.35	0.4	1.1
0.25	0.53	-0.8	-0.4	-0.13	0.42	0.75
0.13	-1.31	-0.18	-0.73	0.23	0.79	0.1
0.13	0.58	0.69	1.96	0.13	0.39	0.42
0.1	0.13	-0.67	-0.44	0.03	0.7	0.72
0.28	0.1	-0.13	0.35	-0.28	0.8	0.61

because it will return lines with velocity of 0.13. With regular expressions, we can restrict the search to the first “column”.

grep -P '^0\.13' snap.txt

0.13	-0.87	0.25	-1.11	0.24	0.98	1.23
0.13	0.0	-0.1	-0.32	-0.49	0.46	1.16
0.13	1.09	-0.66	0.41	0.21	0.24	0.02
0.13	1.16	0.45	1.37	0.3	0.08	0.87
0.13	0.72	-0.36	0.9	0.34	0.59	0.94
0.13	0.21	-0.53	-0.74	0.12	0.61	1.38
0.13	-1.19	-0.05	-0.82	0.73	0.32	1.36
0.13	-0.03	-0.22	-1.32	0.35	0.4	1.1
0.13	-1.31	-0.18	-0.73	0.23	0.79	0.1
0.13	0.58	0.69	1.96	0.13	0.39	0.42

If we want to find particles with mass of 3 solar mass, we could try

grep -P '^3' snap.txt

3.01	0.18	-0.22	-1.25	0.1	0.42	1.0
34.38	-1.15	-0.25	-0.9	0.14	0.55	1.23

Note that this will return

34.38	-1.15	-0.25	-0.9	0.14	0.55	1.23

We need to elaborate a bit more on our regular expression. One more reliable regular expression is

grep -P '^3\.' snap.txt

3.01	0.18	-0.22	-1.25	0.1	0.42	1.0

If we want to find particles with vx of 0.16, we could try

grep -P '^.*\t.*\t.*\t.*\t0.16' snap.txt

0.35	-0.16	0.02	-0.05	0.16	1.15	1.11
0.14	0.82	0.47	1.15	0.16	0.91	0.64
0.11	1.16	-0.5	0.52	0.11	0.68	0.16
0.18	-1.36	-0.27	-0.73	0.16	0.81	0.93
0.18	0.17	-0.51	-0.76	0.16	0.3	1.42
0.25	1.45	0.21	0.32	0.16	0.45	1.11
0.36	0.84	0.1	0.99	0.16	0.38	1.02
0.11	0.22	-0.5	-0.71	0.16	-0.02	0.5
0.18	0.85	0.04	0.82	0.16	0.74	0.89
0.41	-0.01	-0.32	-1.36	0.16	-0.01	1.13
1.83	0.23	-0.51	-0.79	0.06	0.16	1.28

Note the lines

0.11	1.16	-0.5	0.52	0.11	0.68	0.16

and

1.83	0.23	-0.51	-0.79	0.06	0.16	1.28

We could fix it using

grep -P '^(.{3,5}\t){4}0.16' snap.txt

0.35	-0.16	0.02	-0.05	0.16	1.15	1.11
0.14	0.82	0.47	1.15	0.16	0.91	0.64
0.18	-1.36	-0.27	-0.73	0.16	0.81	0.93
0.18	0.17	-0.51	-0.76	0.16	0.3	1.42
0.25	1.45	0.21	0.32	0.16	0.45	1.11
0.36	0.84	0.1	0.99	0.16	0.38	1.02
0.11	0.22	-0.5	-0.71	0.16	-0.02	0.5
0.18	0.85	0.04	0.82	0.16	0.74	0.89
0.41	-0.01	-0.32	-1.36	0.16	-0.01	1.13

Alternatives

Select the lines of gapminder_data.csv that have Europe or Asia.

Solution

grep -P "(Europe|Asia)" gapminder_data.csv

Key Points

  • grep selects lines in files that match patterns.

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