Lecture 6 - Puzzle time! (Regular Expressions)

Essential Skills For Computational Biology

2020-06-30

Kevin Bonham, PhD

Strings contain patterns

Here's a typical list of files from a DNA sequencing run:

sequences = [
    "C0005-3F_L001_R1_001.fastq.gz",
    "C0005-3F_L001_R2_001.fastq.gz",
    "C0005-3F_L002_R1_001.fastq.gz",
    "C0005-3F_L002_R2_001.fastq.gz",
    "C0016-3E_L001_R1_001.fastq.gz",
    "C0016-3E_L001_R2_001.fastq.gz",
    "C0016-3E_L002_R1_001.fastq.gz",
    "C0016-3E_L002_R2_001.fastq.gz",
]

8-element Array{String,1}:
 "C0005-3F_L001_R1_001.fastq.gz"
 "C0005-3F_L001_R2_001.fastq.gz"
 "C0005-3F_L002_R1_001.fastq.gz"
 "C0005-3F_L002_R2_001.fastq.gz"
 "C0016-3E_L001_R1_001.fastq.gz"
 "C0016-3E_L001_R2_001.fastq.gz"
 "C0016-3E_L002_R1_001.fastq.gz"
 "C0016-3E_L002_R2_001.fastq.gz"

##Simple Patterns:

• abc matches literal "abc"
• [abc] matches any one of a, b, or c
• [^abc] matches any character except a, b, or c
• [a-z0-9] matches any lowercase letter or digit

Puzzle: https://regexr.com/57ijc

##Repeating Patterns:

• + matches 1 or more of a pattern
  • eg. [0-9]+ matches one or more digits
• * matches 0 or more of a pattern
• ? matches 0 or 1 of a pattern
• {N} matches N of a pattern
  • eg. [abcdr]{4} matches abra and cada, but not abracadabra
  • Can also to ranges; {2,4} matches 2 to 4, {3,} is 3 or more

Puzzle: https://regexr.com/57ik4

Special Patterns:

• . matches any character, except a new line
• \w matches any word character (same as [A-Za-z0-9_])
• \d matches any digit (same as [0-9])
• \s matches any whitespace (space, tab, newline, etc)
• If you need to match a character that is otherwise special, "escape" it with \
  • eg. to match a literal period, \.

Puzzles:

• https://regexr.com/57ikd
• https://regexr.com/57ikg

More fun with regular Expressions

• Use the regexr cheatsheet (or find another one - they're all over)
  • There are a lot more patterns that can be used
• https://regexcrossword.com/
• My most complicated regex to date:

^([`~]{3,})(?:(?:(?:\\{|\\{\\.|)(julia)(?:;|))|(@(docs|autodocs|ref|meta|index|content|example|repl|eval|setup|raw)))\\s*(?:.*?)(\\}|)\\s*$

Some people, when confronted with a problem, think "I know, I'll use regular expressions." Now they have two problems.

Regular expressions in julia

for seq in sequences
    m = match(r"^([MC]\d+\-[0-9][EF])_L00.+fastq\.gz", seq)
    println(m.captures[1])
end

C0005-3F
C0005-3F
C0005-3F
C0005-3F
C0016-3E
C0016-3E
C0016-3E
C0016-3E

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