Introduction to Regular Expressions

2020-03-18

Supriya Khedkar & Toby Hodges

Download example files here: https://oc.embl.de/index.php/s/kQavCkbomGu4zyM

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Sign-in

Please add your name below

  • Patrick Hasenfeld
  • Jia Le Lim
  • Laura R. de la Ballina
  • Patricia Carvajal
  • Pamela Ferretti
  • Loukia Georgatou-Politou
  • Luca Santangeli
  • Jesus Alvarado
  • Umut Yildiz
  • Martin Gutierrez
  • Tafsut Tala-Ighil
  • Biruhalem Taye
  • Abi Wood
  • Christopher Hall
  • Silvia Natale
  • Anusha Gopalan
  • Kimberly Meechan
  • William Andrés López Arboleda
  • Renato Alves
  • Katharina Zirngibl
  • Filipa Torrao
  • Mariya Timotey Miteva

Markdown essentials

and multiple
lines
of code
with triple backticks
on their own lines

import numpy

def print_explanation:
    explanation = '''
    you can even turn on syntax highlighting for
    most languages by naming the language immediately
    after the opening three backticks
    '''
    print(explanation)

Notes

please use this area to take notes throughout the course

Introduction

  • Regular expressions are a way to describe patterns in text.
  • Can be used in many different applications
  • You can use them in Microsoft Word

Example: how to identify a phone number in a long document? (set of 12 numbers) Search for each occurence of 0, or generate all possible 12-digit long numbers ? Too long.
Use a token describing the the phone number, and looking for the pattern of a 12-digit long number, whatever its value.
Needs a regular expression engine: tools learnt today will be applicable to mutliple programming languages.
install a text editor like notepad++, atom, textwrangler, …

https://regex101.com/

  • Can give a text string as an input and a character string (regular expression) to look for, in this document.
  • Is able to look for RE in texts, but not to replace them: need to use a text editor.

Fundamentals

regex101.com

  • copy & paste content of example.gff file
  • search for HDAC (can also search for numbers)
  • search is case sensitive (to make it case insensitive, with certain languages, we can use -i)

Exercise 2.1

Find every instance of a histone deacetylase (HDAC) in the file, based on the gene name.
Are there any potential problems with your search? Think about how you might make your search as specific as possible, to avoid spurious matches.
If there are any repeats of 'HDAC' in a field other than gene name, that could be problematic. To reduce spurious matches, we could search specifically for Name=HDAC to specify the field as well as the value.
How to combine a search
To look for HDAC1 and HDAC2 at the same time, enter Name=HDAC[12]. It will not fetch HDAC12 (will be a partial match of the first 5 characters)

Can also give ranges: [A-Z],[0-9]

Exercise 2.2

a) In total, how many lines mention HDAC 1-5 in example.gff? Solution: Name=HDAC[1-5]
To avoid that HDAC11-59 are recognized, we can add a ^ which prevents the matching Name=HDAC[1-5][^0-9]
To look for the character string 1-5 and not the range of numbers between 1 and 5, insert a hyphen before 1-5 to specify that you are not looking for a range: Name=HDAC[-1-5]

b) Which of the following expressions could you use to match any four-letter word beginning with an uppercase letter, followed by two vowels, and ending with 'd'?

	i) [upper][vowel][vowel]d  

	ii) [A-Z][a-u][a-u]d

	iii) [A-Z][aeiou][aeiou]d

	iv) [A-Z][aeiou]*2;d

c) Try playing around with the character ranges that you have learned above. What does [A-z] evauluate to? What about [a-Z]? Can you create a range that covers all letter and number characters?

Solution:[A-z] will match all letters, not depending on the case.
To have all letter and number characters: [A-z0-9]
[0-z] will also work, because characters are ordered as: numbers, uppercase letters, lowercase letters.
i
ii
iii xxXxxXxxxxxxx
iv

e.g. [upper][vowel][vowel][d] would match "pwld" (because 'p' is in the first set, w in the second, l in the third)

Please type 'X' under this line when you're done with these exercises
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When specifying character ranges such as [1-z] the order assumed is based on the ASCII table.
The order is: !"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~.

Exercise 2.3

Use an inverted set to only match the human autosomes (chr1-22), i.e. filtering out chromosomes chrX, chrY and chrM. How many records with autosomes can you find in file example.gff?

Please type 'X' under this line when you're done with these exercises

Xxxxx
Solution: chr[^XYM]

Summary: Sets and Ranges

Groups of characters that can be matched in a certain position are specified between []
• Letters, numbers, symbols [&k8Y]
• Uppercase [A-Z]
• Lowercase [a-z]
• Numbers [0-9]
More examples:
• [N-Z]
• [5-9]
• [a-f0-9]

For inverted sets (non-matching characters) use ^ as shown here [^268]

Tokens & Wildcards

Token Matches Set Equivalent
\d Any digit [0-9]
\s Any whitespace character (space, tab, newlines) [ \t\n\r\f]
\w Any 'word character' - letters, numbers, and underscore [A-Za-z0-9_]
\b A word boundary character n/a
\D The inverse of \d i.e. any character except a digit [^0-9]
\S Any non-whitespace character [^ \t\n\r\f]
\W Any non-word character [^A-Za-z0-9_]

Exercise 3.1

Match dates of the form 31.01.2017 (DAY.MONTH.YEAR) in the example file person_info.csv. Pay attention to not wrongly match phone numbers. How many matches do you find?

Please type 'X' under this line when you're done with these exercises
xxxxxxxxxxxTest-gist.md

Test

xxx

Solution: \d\d[.]\d\d[.]\d\d\d\d or \d\d\.\d\d\.\d\d\d\d
Note: . any character, . the dot character

Exercise 3.2

How can you refine the regex from the previous exercise to prevent matching strings with preceding or succeeding digits, such as 131.01.20171?
Solution: \b\d\d\.\d\d\.\d\d\d\d\b

Exercise 3.3

When designing a regular expression to match exactly four digits, what would be the difference between using the two regular expressions \b\d\d\d\d\b and \D\d\d\d\d\D?
Solution: \D\d\d\d\d\D also matches non-digit flanking characters
Please type 'X' under this line when you're done with these exercises
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Exercise 3.4

Count how many sequences in example_protein.fasta are of transcript_biotype "protein_coding". Hint: sequence records have a header that starts with the character ">".

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Repeats

Symbol Behaviour Example Matches Doesn't Match
+ Match one or more of preceding character/set AGC+T AGCCCT AGT
? Match zero or one of preceding character/set AGC?T AGT AGCCT
* Match zero or more of preceding character/set AGC*T AGCCCCCT AGG

Excercise 4.1

a) Which of the follow strings will be matched by the regular expression MVIA*CP?

​i) MVIAACP  

​ii) MVICP  

​iii) MVIACP  

​iv) all of the above

a)

i)
ii)
iii)
iv) xxxxxx

b) Write a regular expression to match the string

"ATGCTTTCG"

and

"ATCTCG"

but not

"ATGGCCG"

Solution: ATG?CT+CG

Please type 'X' under this line when you're done with these exercises
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Exercise 4.2

use {} to search example_protein.fasta for trytophan (W)
followed by tyrosine (Y), with an increasing number of leucine (L)
residues in between. Start by searching for this pattern with three leucines (i.e. 'WLLLY'), then reduce this to two, and one. Is this working as you expect? How would you search for a range of lengths of the leucine repeat? Try searching for any patterns with at between one and four leucines.
What happens if you leave out the upper limit inside the {}? Or the lower limit? Can you leave out both?

Please type 'X' under this line when you're done with these exercises
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Solution: WL{1,4}Y
Note: [] - set
() - group
{} - number of occurences of preceding character/set, can also have upper an lower limit, like {1,3}

Capture Groups

Example: reorder band names alphabetically. To do so, we need to put "The" at the end of each line.
First: select the lines that we want to reframe
Capture groups because we can capture a region of the input, and reuse it for the replacement value
To define a capture group, put it in parenthesis: (+)
To reintroduce it in the replacement line: $1 or \1
Limited to 9 capture groups.

Exercise 5.1

The file example_protein_malformed.fasta is missing the > character at the beginning of the headers. Use a capture group to add them.

Solution:
(^ENSP.+) regex for identifying and grouping

$1 for subsitution

Exercise 5.2

The file file_paths.txt contains file paths of image files. The files are organised by folders based on vacations, but the files themselves have cryptic names. You want the files to be prefixed by the vacation and move them into a shared folder. At the end the list should look like:

/Users/Jane/shared/vacation-pics/France-2015-IMG-06650.jpg
/Users/Jane/shared/vacation-pics/France-2015-IMG-06651.jpg
...
/Users/Jane/shared/vacation-pics/France-2017-IMG-08449.jpg
...
/Users/Jane/shared/vacation-pics/Greece-2016-IMG-07895.jpg
...

Use a capture group to transform the file paths accordingly.

Solution: Pictures/(w±\d{4})/(IMG-\d+.jpg)
Substitution:
shared/vacation-pics/$1-$2

Tip: When designing regular expressions be as specific as possible, greedy regular expression definitions like .+ could cause problems

Alternative Matching

Example: Homo Sapiens|Mus Musculus: enables to look for both: the | signifies "or"

Exercise 6.1

If you study the contents of the file person_info.csv, you will see that some variation exists in the address formatting. For example, some of the addresses use 'First Street' while others use '1st Street' or some other variation.
Can you find all the lines containing information on a person living on 1st/First Street/street, using a single regular expression?

Solution(s):[Ff]irst [Ss]treet|1st [Ss]treet
([F|f]irst|1st)\s([Ss]treet)

Please type 'X' under this line when you're done with these exercises
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Exercise 6.2

The FASTQ file example.fastq contains sequence reads with quality scores, in the format

@sequence header line with barcode sequence
sequence
+
quality scores for basecalls

Unfortunately, the barcode sequences in the header lines are wrong, and the barcodes are still attached to the front of the sequences. There are three barcodes that we are interested in: AGGCCA, TGTGAC, and GCTGAC.

a) how many reads are there in the file for each of these barcodes?

Solution:
AGGCCA: 25
TGTGAC: 29
GCTGAC: 19

b) write a regular expression that will find and these barcodes and a replacement string that will remove them from the start of the sequences in which they are found

Solution:^(AGGCCA|TGTGAC|GCTGAC)
Replacement string: nothing, because we want to remove this region

c) of course, the format of the file means that you should probably remove the quality scores associated with those sequence positions too. Rewrite your regex so that the barcode sequence AND its corresponding quality scores (i.e. the first six characters on the sequence and quality lines) are removed.

Solution: ^(AGGCCA|TGTGAC|GCTGAC)([ATGCN]+\n\+\n)(.{6})
Replacement string: $2
d) finally, can you build on the regex and replacement string from part c), to replace the incorrect index sequences in the header lines with the barcodes for each relevant sequence record?

Solution: (\d:\w:\d:)[ATGCN]{6}\n(AGGCCA|TGTGAC|GCTGAC)([ATGCN]+\n\+\n)(.{6})
Replacement: $1$2\n$3

Tip: to group character strings, to apply "or", but not consider the group as one, use ?: at the beginning of the parenthesis as so: (?:)

Please type 'X' under this line when you're done with these exercises
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Feedback

https://de.surveymonkey.com/r/denbi-course?sc=hdhub&id=000259

In question 11, we would particularly love to hear about what we could do to improve the way we teach online in the future - we will probably need to do this a lot in 2020! :)

Applied Examples

Command line

perl -ane '<perl expression>'

  • -a: automatically split string into groups based on delimiter (default delimiter is whitespace, I think)
  • -n: parse every line
  • -e <perl_expression>: run perl_expression on every line

It is Very Important to use single quotes around your Perl expression

R:x xxxX
Python: XXxx

R

To use regular expressions in R one could use stringr package (on its own and also in combinationtion with tidyverse)

Most of the commands that we learned today work with stringr (ofcourse with a need to use "\w") as shown in this cheat-sheet http://edrub.in/CheatSheets/cheatSheetStringr.pdf

stringr commands can be used with filter (tidyverse command)

For example: Solution to applied examples question 1 with stringr would be -
'data %>% filter(str_detect(Organism_name,"^Vibrio_*"))'

Python

  • as with everything in Python, regular expressions are all about objects!
  • you need to import re (a module from the standard library) to work with them
  • use raw strings to describe your regex pattern - type 'r' before you open the string
    • this saves you from Backslash Hell
    • e.g. r'\w\s[A-Z]', which is equivalent to '\\w\\s[A-Z]'
  • two approaches you can take:
    • compile a regex object with re.compile(pattern)
    • use functions and pass pattern as an argument
  • regex object option:
import re

pattern = r'example pattern goes here'
regex_object = re.compile(pattern)
dir(regex_object)
# match: see if regex matches *at the start* of the target string
# search: see if regex matches exist anywhere in target string
# findall: returns list of substrings matching regex from target string
# finditer: as above, but returns iterator instead of list

print(regex_object.match('example string without match goes here'))
print(regex_object.match('example string with match goes here'))
  • more about match objects later…
  • regex functions option:
import re
pattern = r'example pattern goes here'
print(re.match(pattern, 'example string with match goes here'))
print(re.search(pattern, 'example string with internal match goes here'))
  • if a match is found, a match object is returned (otherwise, None)
    • have several useful methods
pattern = r'[A-Z][a-z]{4:6}'
patternObj = re.compile(pattern)
matchObj = patternObj.match('Where are we going?')
matchObj.group()
matchObj.start()
matchObj.end()
matchObj.span()
  • as None is returned when no match is found, use if/else to handle multiple patterns
import re
m = re.match(r'\d\d-\d\d-2019', ' 04-09-2019')

if m:
    print('Match found: ', m.group())
else:
    print('No match')
  • if using capture groups, the group method becomes more interesting
import re

pattern = r'([CG]{3})+(TATA[AT]A[AT])([CG]+)'
match = re.match('CGCTATAAAAGGGC')
match.group()
match.group(0)
match.group(2)

(feel free to add your own)

Copy of Zoom Chat

10:29:37 From Toby : a few people may still not have the link to the notes, in which case - https://hackmd.io/@JKgItcTtSZmVTddVipOPMA/regex2020/edit
10:35:51 From Pamela_Ferretti : /hand
10:35:58 From Pamela_Ferretti : Can you repeat? This last aprt
10:36:00 From patrick hasenfeld : why the hyphen?
10:36:03 From Pamela_Ferretti : yes
10:36:07 From Silvia : Where are questions exercise?
10:36:37 From Silvia : The file
10:37:09 From Toby : The exercises are added to the notes as we go along
10:37:26 From Toby : these exercises start at line 108
10:38:56 From Laura : /hand
10:42:29 From Jia Le Lim : Quick question, is the \ necessary in front of the d => like \d
10:43:08 From Jia Le Lim : Ah okay, thank you
10:45:18 From Anusha Gopalan : /hand
10:45:36 From patrick hasenfeld : interestingly [1-z] also matches uppercase letters
10:46:07 From Toby : it does!
10:59:20 From Renato Alves : I added a note about the order of the characters in ranges such as [1-z] to the collaborative document.
11:05:20 From supriya : I have added summary of the regex fundamentals to the shared document
11:06:13 From Toby : exercise on line 144
11:08:48 From Jia Le Lim : chr[^XYM]
11:08:56 From Anusha Gopalan : chr[^oMXY]
11:11:03 From Patricia Carvajal : /hand
11:11:27 From Patricia Carvajal : chr[0-9] matches only one character after chr
11:11:46 From Patricia Carvajal : how do we match x number of characters?
11:12:14 From Laura : /hand. Sorry, just one question. Is ^ both a gap and a negation?
11:20:08 From Anusha Gopalan : /hand : why isn’t it matching the second instance from “is an..”
11:21:09 From Anusha Gopalan : thank you!
11:27:37 From Jia Le Lim : /hand : is \bis\b equivalent to ^is$
11:31:20 From Jia Le Lim : Thank you!
11:31:49 From Festus Nyasimi : how do you match ^ in a line
11:37:06 From Festus Nyasimi : And again matching ^ at the start of a line
11:44:07 From Anusha Gopalan : \hand: So both . And [.] match literally “.”?
11:44:07 From Patricia Carvajal : /hand
11:44:50 From Patricia Carvajal : I got a little lost, how would you match a character "^" at the end of a line?
11:45:23 From Anusha Gopalan : It doesn’t define a particular ascii?
11:46:37 From Festus Nyasimi : the . can't be escaped in a set?
11:46:38 From Jia Le Lim : ^$ ?
11:47:21 From Patricia Carvajal : thanks!!
12:09:13 From Martin Gutierrez : /hand could you explain what ? does again?
12:10:05 From Martin Gutierrez : ok thanks!
12:19:35 From patrick : could youshow the exercide again?
12:25:13 From Pamela_Ferretti : As you prefer
12:25:15 From Pamela_Ferretti : :)
12:25:21 From patrick : yes
12:28:03 From Patricia Carvajal : /hand
12:28:21 From Patricia Carvajal : can't unmute the mic
12:28:23 From Patricia Carvajal : ok
12:28:35 From Patricia Carvajal : T{3}, would match 3 Ts
12:28:53 From Patricia Carvajal : {1,3} what does it indicate?
12:29:29 From Patricia Carvajal : thanks
12:29:57 From Anusha Gopalan : /hand : can you look for repeats of combinations of characters - like TA repeating three times a sequence like GCCTATATACGGA ?
12:29:59 From Patricia Carvajal : yes, it does
12:29:59 From Mariya to Toby (Privately) : yes Toby this is the keyboard - Alt+è
do not work, also +è do not work
12:30:43 From Anusha Gopalan : Ok thank you
12:30:58 From jesus alvarado : (AT){3}?
12:33:22 From jesus alvarado : See you
12:33:29 From Toby : back at 13:33
12:33:39 From Renato Alves : Enjoy lunch /bye
12:34:01 From Patricia Carvajal : Enjoy
12:34:16 From Luca Santangeli : Enjoy :)
13:38:57 From supriya : We are at exercise 4.2 (shared document line251)
13:42:19 From Laura : /hand. Sorry, could you say the answer to the last part of the exercise? What happens if you leave out the upper limit inside the {}? Or the lower limit? Can you leave out both?
14:00:27 From Silvia : Is it possible to copy and paste everything in excel?
14:02:33 From Toby : @Silvia: are you asking whether it’s possible to use regular expressions in Excel, or suggesting that the kind of “group_1, group_2, group_3” reorganisation would be possible with Excel too?
14:04:05 From Silvia : Since your answer.. both :)
14:05:06 From Toby : the answer to 1. is “yes, I think so, but it looks kinda complicated to set up”: https://analystcave.com/excel-regex-tutorial/
14:07:04 From Toby : and to 2: yes, this kind of example, where every line looks the same and groups are anyway separated by some standard character e.g. “,” can be solved easily enough with Excel too. But that approach is less useful where the pattern only occurs on a selection of lines, and/or where the patterns appear at unpredictable points in the line(s)
14:07:46 From Toby : (see the FASTA file in the exercise for example)
14:09:46 From Silvia : Thank you!
14:10:24 From Patricia Carvajal : identifies well, but I have not been able to add the simbol ">" at the substitution part
14:17:49 From patrick : - is not in w+
14:19:12 From Renato Alves : Careful that the . in .jpg needs to be escaped.
14:23:51 From Anusha Gopalan : /hand
14:24:28 From Christopher Hall : /hand can I count the / and choose between them in Regex, or this a problem for slices and programming languages
14:27:40 From patrick : /hand for dcumentation, whats was the term if you use loose regeular expressions lie .+ and not specific ones
14:28:01 From Renato Alves : greedy was the word Toby used
14:28:10 From patrick : thanks
14:30:54 From Patricia Carvajal : what file is this one?
14:31:24 From Toby : we don’t have a file for this, sorry.
14:32:05 From Patricia Carvajal : ok, thanks
14:32:18 From Toby : I’ve pasted it at the bottom of the shared notes (line 338)
14:32:29 From Toby : in case you want to use exactly what Supriya had
14:40:11 From Anusha Gopalan : /hand
14:40:21 From Laura : I think you are also missing the first F
14:41:49 From Filipa : could we do it like this? or is it not safe? (1st|First) (Street|street)
14:42:20 From Patricia Carvajal : how about ([F|f]irst|1st)\s([Ss]treet)
14:42:50 From Filipa : ah yes, ok thank you
14:43:04 From Toby : I like Patricia’s
14:43:06 From Festus Nyasimi : ([Ff]irst|1st) ([sS]treet|[Aa]ve)
14:43:11 From Toby : think it would work
14:51:08 From Patricia Carvajal : /hand
14:51:13 From Patricia Carvajal : we used
14:51:28 From Patricia Carvajal : | for some sort of an "or" expression
14:51:46 From Patricia Carvajal : do we have an equivalent for "and"
14:51:47 From Patricia Carvajal : ?
14:52:45 From Toby : “and” would be an extension of the regular expression i.e. “patternApatternB” is effectively the same as “patternA AND patternB” already
14:54:36 From Patricia Carvajal : it would be more like a "starts with AND finishes with" (regardless on what's in the middle)
14:57:28 From Renato Alves : Patricia: in the example Toby mentioned you can use "patternA.*patternB" the dot represents any character and * as many matches as possible.
15:00:19 From supriya : Patricia you could also use anchor to denote begins with and ends with and * for any characters in between as Renato suggested above
15:01:57 From patrick : the quality line is not \w
15:02:01 From Festus Nyasimi : The quality scores are mostly symbols
15:08:35 From patrick : why is $1 the whole line, you just capered the last part of the string
15:14:51 From Festus Nyasimi : How do group counting occur when groups are embedded in groups
15:16:24 From Toby : https://de.surveymonkey.com/r/denbi-course?sc=hdhub&id=000259
15:18:31 From supriya : file_applied_examples_proks.txt
15:18:36 From Toby : @Festus: from the order that the opening parentheses appear
15:18:51 From supriya : exercise_applied_examples.txt
15:19:26 From Festus Nyasimi : Thanks
15:19:48 From Toby : i.e. with (fes(tus ny)asim)i $1 = festus nyasim & $2 = tus ny
15:20:05 From Toby : see here for more info https://stackoverflow.com/questions/1313934/how-are-nested-capturing-groups-numbered-in-regular-expressions
15:20:59 From Renato Alves : See also https://www.regular-expressions.info/named.html if you prefer to use a name or tag instead of $1, \(2, .... 15:21:34 From Toby : +1 thanks, Renato 15:22:30 From Laura : /hand, in my computer it says regex command not found, do we need to install something before? 15:25:01 From Toby : the “mac-bork35:regex khedkar\)” part is Supriya’s prompt - you shouldn’t type this part
15:25:15 From Toby : (the command begins at “cat …”)
15:25:20 From Laura : I’ve just realised that, sorry :)
15:25:25 From Laura : Got confused
15:25:26 From Toby : no worries
15:26:39 From Patricia Carvajal : sorry, got confused on the perl part
15:27:00 From Toby : could you explain the option flags again?
15:27:31 From patrick : maybe with awk
15:27:32 From Laura : No, no I got confused
15:28:51 From patrick : is F[0] the first element of the line?
15:32:45 From patrick : lookd like a japanese emoji
15:32:56 From Toby : haha
15:35:19 From Toby : “the file itself is not clean” is the tagline of “Bioinformatics: The Movie”
15:35:26 From Toby : :(
15:36:11 From Laura : /hand
15:36:12 From patrick : are you mossing the genus_family_ATCC lines?
15:36:20 From patrick : *missing
15:37:19 From Toby : to learn more about this, you might want to read our Linux command line course materials :)
15:37:20 From patrick : no worries, they are includes
15:37:36 From Toby : https://bio-it.embl.de/course-materials/
15:37:56 From Patricia Carvajal : I have to go. Thanks a lot for the course =)
15:38:29 From Laura : Great, thanks!
15:40:20 From Martin Gutierrez : I have to leave. Thanks for the great course!
15:46:51 From william A. lópez : Sorry
16:00:36 From Toby : https://de.surveymonkey.com/r/denbi-course?sc=hdhub&id=000259
16:01:10 From patrick : thanks, very well presented
16:01:13 From Umut Yildiz : Thanks for the course! See you!
16:01:26 From Katharina Zirngibl : Thank you very much!!
16:01:27 From Laura : Thanks a lot!! =)
16:01:29 From user : Thank you very much!
16:01:29 From jesus alvarado : Thanks!!
16:01:30 From Renato Alves : Wooo! Thanks Suprya and Toby
16:01:31 From william A. lópez : Thanks
16:01:35 From Jia Le Lim : Bye! Thanks!

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