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Eric Coissac
369
web_src/lectures/computers/regex/slides_regex.qmd
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web_src/lectures/computers/regex/slides_regex.qmd
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---
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title: "Regular Expressions"
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format:
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revealjs:
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theme: beige # thème des slides
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transition: fade # effet de transition entre les slides
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---
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## Regular Expressions
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Pattern matching for text with variations
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Example: `tot*o` matches:
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- "to" + any number of "t" + "o"
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- "toto", "totto", "totttto", etc.
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---
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## Basic Concepts
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**Alphabet**: Set of allowed symbols
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- DNA: {A, C, G, T}
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- Text: {letters, digits, punctuation, ...}
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**Text**: Sequence of symbols from alphabet
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**Word**: Subsequence of consecutive symbols
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---
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## Simple Regular Expression
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`ATG` matches exactly "ATG"
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```{mermaid}
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graph LR
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D((D)) -->|A| 1((1))
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1 -->|T| 2((2))
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2 -->|G| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Symbol Ambiguities
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### Any Character: `.`
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`.TG` matches:
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- "ATG", "TTG", "GTG", "CTG", ...
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```{mermaid}
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graph LR
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D((D)) -->|any| 1((1))
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1 -->|T| 2((2))
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2 -->|G| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Character Classes
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`[ATG]TG` matches only:
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- "ATG", "TTG", "GTG"
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```{mermaid}
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graph LR
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D((D)) -->|A/T/G| 1((1))
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1 -->|T| 2((2))
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2 -->|G| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Ranges and Negation
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**Ranges**: `[A-Z]`, `[0-9]`, `[A-Za-z0-9]`
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**Negation**: `[^A-Z]` (anything except uppercase)
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---
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## Repetition: Zero or One
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`ballons?` matches:
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- "ballon" (singular)
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- "ballons" (plural)
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```{mermaid}
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graph LR
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D((D)) -->|b| 1((1))
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1 -->|a| 2((2))
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2 -->|l| 3((3))
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3 -->|l| 4((4))
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4 -->|o| 5((5))
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5 -->|n| 6((6))
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5 -->|s| 7((7))
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7 -->|n| F((F))
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6 --> F
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Repetition: Zero or More
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`TTA*TT` matches:
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- "TTTT", "TTATT", "TTAAATT", ...
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```{mermaid}
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graph LR
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D((D)) -->|T| 1((1))
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1 -->|T| 2((2))
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2 -->|A| 2
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2 -->|T| 3((3))
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3 -->|T| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Repetition: One or More
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`TTA+TT` matches:
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- "TTATT", "TTAATT", "TTAAATT", ...
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- But NOT "TTTT"
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```{mermaid}
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graph LR
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D((D)) -->|T| 1((1))
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1 -->|T| 2((2))
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2 -->|A| 3((3))
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3 -->|A| 3
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3 -->|T| 4((4))
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4 -->|T| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Exact Repetition
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`A{3,5}` matches:
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- "AAA", "AAAA", "AAAAA"
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`A{3}` matches exactly "AAA"
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---
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## Special Characters
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- `^` - Start of line
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- `$` - End of line
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- `\n` - Newline
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- `\t` - Tab
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Examples:
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- `^start` - "start" at beginning of line
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- `end$` - "end" at end of line
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- `^exact$` - "exact" as entire line
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---
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## Alternation
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`papa|mama` matches either:
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- "papa" OR "mama"
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```{mermaid}
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graph LR
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D((D)) -->|p| 1((1))
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1 -->|a| 2((2))
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2 -->|p| 3((3))
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3 -->|a| F1((F))
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D -->|m| 4((4))
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4 -->|a| 5((5))
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5 -->|m| 6((6))
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6 -->|a| F2((F))
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style D fill:#90EE90
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style F1 fill:#FFC0CB
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style F2 fill:#FFC0CB
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```
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---
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## Grouping
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`T(AA|AG|GA)` matches:
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- "TAA", "TAG", "TGA"
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Instead of incorrect: `TAA|AG|GA`
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---
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## Backreferences
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`([ACGT]{3})\1{9,}` matches:
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- Any triplet repeated 10+ times
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- Example: "CAGCAGCAGCAG..."
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---
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## Quick Reference
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### Symbol Ambiguity
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| Pattern | Matches |
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|---------|---------|
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| `.` | Any character |
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| `[abc]` | a, b, or c |
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| `[^abc]` | Not a, b, or c |
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### Repetition
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| Pattern | Matches |
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|---------|---------|
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| `?` | 0 or 1 |
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| `*` | 0 or more |
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| `+` | 1 or more |
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| `{n,m}` | n to m times |
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---
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## Biological Application: Gene Finding
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Find Coding Sequences (CDS) in bacterial DNA:
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1. Start codon
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2. Multiple non-stop codons
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3. Stop codon
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---
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## Start Codons
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Bacterial start: ATG, TTG, GTG
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Pattern: `[ATG]TG`
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```{mermaid}
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graph LR
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D((D)) -->|A/T/G| 1((1))
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1 -->|T| 2((2))
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2 -->|G| F((F))
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Stop Codons
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Bacterial stop: TAA, TAG, TGA
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Pattern: `T(A[AG]|GA)`
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```{mermaid}
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graph LR
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D((D)) -->|T| 1((1))
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1 -->|A| 2((2))
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2 -->|A/G| F1((F))
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1 -->|G| 3((3))
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3 -->|A| F2((F))
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style D fill:#90EE90
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style F1 fill:#FFC0CB
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style F2 fill:#FFC0CB
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```
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---
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## Non-Stop Codons
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61 codons that aren't stop codons
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Pattern: `[ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT])`
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```{mermaid}
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graph LR
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D((D)) -->|A/C/G| A1((1))
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A1 -->|A/C/G/T| A2((2))
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A2 -->|A/C/G/T| F1((F))
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D -->|T| B1((3))
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B1 -->|C/T| B2a((4))
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B2a -->|A/C/G/T| F2((F))
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B1 -->|G| B2b((5))
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B2b -->|C/G/T| F3((F))
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B1 -->|A| B2c((6))
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B2c -->|C/T| F4((F))
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style D fill:#90EE90
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style F1 fill:#FFC0CB
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style F2 fill:#FFC0CB
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style F3 fill:#FFC0CB
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style F4 fill:#FFC0CB
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```
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---
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## Complete CDS Pattern
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`[ATG]TG([ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT]))+T(A[GA]|GA)`
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- Start codon
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- 1+ non-stop codons
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- Stop codon
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```{mermaid}
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graph LR
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D((D)) -->|A/T/G| 1((1))
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1 -->|T| 2((2))
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2 -->|G| 3((3))
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3 --> 4((4))
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4 -->|A/C/G| 5((5))
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5 -->|A/C/G/T| 6((6))
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6 -->|A/C/G/T| 7((7))
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4 -->|T| 8((8))
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8 -->|C/T| 9((9))
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9 -->|A/C/G/T| 7
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8 -->|G| 10((10))
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10 -->|C/G/T| 7
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8 -->|A| 11((11))
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11 -->|C/T| 7
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7 --> 4
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7 -->|T| 12((12))
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12 -->|A| 13((13))
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13 -->|A/G| F((F))
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12 -->|G| 14((14))
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14 -->|A| F
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style D fill:#90EE90
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style F fill:#FFC0CB
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```
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---
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## Minimum Length CDS
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`[ATG]TG([ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT])){99,}T(A[GA]|GA)`
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Requires at least 100 amino acids (99 non-stop codons + stop)
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---
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## Summary
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- Regular expressions = text patterns
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- Symbol ambiguity: `.`, `[]`, `[^]`
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- Repetition: `?`, `*`, `+`, `{}`
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- Special chars: `^`, `$`, `\n`, `\t`
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- Powerful for biological sequence analysis
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