Add pedagogic content
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Eric Coissac
335
web_src/05_Lectures/00_Computers/regex/lecture_regex.qmd
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335
web_src/05_Lectures/00_Computers/regex/lecture_regex.qmd
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---
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title: "Regular Expressions"
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format:
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html:
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embed-resources: true # pour que les SVG soient inclus
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self-contained: true # optionnel : tout est intégré dans le HTML
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---
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Regular expressions allow describing a fragment of text by authorizing variations in that text. As an example, $tot*o$ describes a piece of text starting with a "t" then an "o" followed by an undetermined number of "t"s and a final "o". We can therefore consider a regular expression as a pattern of the actual text being searched. To clarify the rest of this text, we'll admit the following definitions:
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## Definitions
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- **Alphabet**: The set of symbols we are allowed to use. For example, DNA is described using a four-letter alphabet ${A, C, G, T}$. Standard UNIX programs using regular expressions (`egrep`, `awk`, etc...) work on a much larger alphabet including all uppercase and lowercase letters, numbers, punctuation marks, and other characters representing formatting actions like line breaks.
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- **Text**: The sequence of symbols corresponding to the analyzed document. A text corresponds to an alphabet. A text can therefore represent very diverse things: a chromosome or protein sequence, the output of another program, a series of descriptions of biological objects such as those obtainable by downloading "flat" files from biological databases.
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- **Word**: A word is a subset of consecutive symbols from a text. This is a more general definition than that of a word in the French language, which gives word status to a group of letters in a text preceded and followed by a space or punctuation mark.
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We'll say that a regular expression is a pattern representing one or more words in a text. Search engines use this pattern to find occurrences of words matching this pattern in a text.
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## The Simplest Regular Expression
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Any piece of text can be considered as a regular expression that recognizes text identical to itself. For example, $ATG$ recognizes the sequence of three letters A, T, G.
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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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## Introducing Ambiguities
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The main interest of regular expressions is their ability to describe words (text fragments) by authorizing certain ambiguities. There are two main classes of ambiguities. The first allows describing alterations on symbols. The second category allows describing the repetition of symbols. Alterations are introduced in the regular expression by using special characters.
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### Symbol Ambiguities
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#### Any Character
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The first special character is the dot ".". It can recognize any character. If we stick to the example of codons, the regular expression `regex{.TG}` recognizes any character followed by a "T" then a "G".
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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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#### A Specific Subset of Characters
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The dot sometimes offers too much flexibility. There's another mechanism to list an authorized group of characters. Just list the authorized characters between brackets "[" and "]". The expression `regex{[ACGT]}` recognizes one of the four letters "A", "C", "G", or "T".
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In bacteria, initiation codons are multiple. Most of the time, codons *ATG*, *TTG*, and *GTG* are recognized as translation initiation codons. These three codons only vary by their first letter, which can be an "A", "T", or "G". The regular expression `regex{[ATG]TG}` recognizes words of three letters starting with a symbol "A", "T", or "G" followed by a "T" and a "G".
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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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#### Any Character Except a Subgroup
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Sometimes it's necessary to describe a set of characters as: "any character of the alphabet except for a particular group of symbols." To describe these negated groups, the same notation is used as for character groups described previously. The only difference is that the group must start with the "^" character. The expression `regex{[^A-Z]}` therefore recognizes any character except an uppercase letter, and `regex{[^b]}` recognizes all characters except "b".
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### Variations on Symbol Repetition
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#### A Symbol Present Zero or One Time
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The simplest alteration on the number of occurrences of a symbol is represented by "?". This character added after the description of a symbol indicates that it can be present or absent in the recognized word. That is, present 0 or 1 times.
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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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#### A Symbol Present an Undetermined Number of Times
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A more flexible form regarding the presence or absence of a symbol in words recognized by a regular expression is provided by the "*" character, which indicates the preceding symbol can be absent or present an undetermined number of times.
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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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#### A Symbol Present at Least Once
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There's syntax that simplifies writing such a constraint. It uses the "+" character as a marker. Thus, the regular expressions `regex{TTA+TT}` and `regex{TTAA*TT}` are strictly equivalent.
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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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#### Describing a Repetition Interval
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A final notation, recently introduced in regular expression syntax, allows giving a lower and upper bound to the number of occurrences of a symbol. The format uses braces "{" and "}" to frame the two bounds.
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### Special Characters
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#### Beginning and End of Line
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By adding a "^" at the beginning of an expression or "$" at the end of an expression, you can force the recognized word to be at the beginning or end of a line.
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#### The Double Meaning of a Character
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Each character has two meanings:
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- A primary meaning: the symbol represented by the character
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- A meta-meaning: Which gives another meaning to the character
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You switch from one meaning to the other by preceding the character with the backslash "\".
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### Combining Multiple Expressions
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The question arises when combining multiple regular expressions with the logical OR operator. I want to build an expression that recognizes the words "papa" or "mama". For this, combine the two simple expressions `regex{papa}` and `regex{mama}` using the "|" character to get the global expression `regex{papa|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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### Subexpressions
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#### Subexpressions and Combination of Multiple Expressions
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It's possible to isolate a subpart of a regular expression using parentheses "(" and ")".
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#### Reusing a Subexpression
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Normally, each step of a regular expression is independent of what happened before in the automaton. It's possible thanks to subexpressions to go against this principle by memorizing a sequence of previous states using a subexpression.
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## Summary of Authorized Alteration Forms
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### Symbol Ambiguity
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| Symbol | Recognizes |
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|--------|------------|
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| . | Any character |
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| [ ] | One of the characters listed between brackets |
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| [^ ] | Any character except those listed between brackets |
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### Repetition Ambiguity
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| Symbol | Number of accepted occurrences |
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|--------|--------------------------------|
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| * | 0 to ∞ |
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| ? | 0 or 1 |
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| + | 1 or more |
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| {x,y} | between x and y occurrences |
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| {x,} | at least x occurrences |
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### Special Characters
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| Symbol | Meaning |
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|--------|---------|
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| ^ at expression start | beginning of line |
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| $ at expression end | end of line |
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| \n | line break |
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| \t | a tabulation |
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## Exercise: Identifying Genes with a Regular Expression
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To identify a CDS, we need to combine three regular expressions: one for the initiation codon, the second for non-stop codons, and the last for stop codons.
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### Start Codons
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In bacteria, there are three start codons: ATG, TTG, and GTG. The corresponding regular expression is: `regex{[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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### Stop Codons
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In most bacteria, there are three different termination codons: TAA (ochre), TAG (amber), and TGA (opale). The regular expression recognizing all stop codons is `regex{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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### Non-stop Codons
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The regular expression recognizing the 61 non-stop codons is:
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`regex{[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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%% État initial
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D((D))
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style D fill:#90EE90
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%% Branche 1: [ACG][ACGT][ACGT]
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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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%% Branche 2: T([CT][ACGT]|G[CGT]|A[CT])
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D -->|T| B1((3))
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%% Sous-branche 2.1: [CT][ACGT]
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B1 -->|C/T| B2a((4))
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B2a -->|A/C/G/T| F2((F))
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%% Sous-branche 2.2: G[CGT]
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B1 -->|G| B2b((5))
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B2b -->|C/G/T| F3((F))
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%% Sous-branche 2.3: A[CT]
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B1 -->|A| B2c((6))
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B2c -->|C/T| F4((F))
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%% États finaux
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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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### Recognizing a Complete CDS
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Recognizing a complete CDS now comes down to assembling the regular expression for starts, that for non-stops (authorizing its repetition), then that recognizing stop codons.
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`regex{[ATG]TG([ACG][ACGT][ACGT]\|T([CT][ACGT]\|G[CGT]\|A[CT]))+T(A[GA]\|GA)}`
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```{mermaid}
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graph LR
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%% État initial
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D((D))
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style D fill:#90EE90
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%% Début: [ATG]TG
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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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%% Boucle principale pour la partie médiane (répétition +)
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3 --> 4((4))
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%% Alternative 1: [ACG][ACGT][ACGT]
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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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%% Alternative 2: T([CT][ACGT]|G[CGT]|A[CT])
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4 -->|T| 8((8))
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%% Sous-alternative 2.1: [CT][ACGT]
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8 -->|C/T| 9((9))
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9 -->|A/C/G/T| 7((7))
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%% Sous-alternative 2.2: G[CGT]
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8 -->|G| 10((10))
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10 -->|C/G/T| 7((7))
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%% Sous-alternative 2.3: A[CT]
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8 -->|A| 11((11))
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11 -->|C/T| 7((7))
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%% Boucle de répétition
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7 --> 4
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%% Fin: T(A[GA]|GA)
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7 -->|T| 12((12))
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%% Alternative finale 1: A[GA]
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12 -->|A| 13((13))
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13 -->|A/G| F((F))
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%% Alternative finale 2: GA
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12 -->|G| 14((14))
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14 -->|A| F((F))
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%% État final
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style F fill:#FFC0CB
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```
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To impose that the CDS codes for a protein of at least 100 amino acids, just replace the "+" sign with a constraint on the minimum number of repetitions of non-stop codons to 99.
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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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372
web_src/05_Lectures/00_Computers/regex/slides_regex.qmd
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372
web_src/05_Lectures/00_Computers/regex/slides_regex.qmd
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@@ -0,0 +1,372 @@
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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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css: ../../slides.css
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transition: slide
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scrollable: true
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theme: beige
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html-math-method: mathjax
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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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## Symbol Ambiguities
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### Any Character: `.`
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`.TG` matches:
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||||
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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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||||
---
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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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||||
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||||
- "ballon" (singular)
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- "ballons" (plural)
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||||
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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))
|
||||
2 -->|l| 3((3))
|
||||
3 -->|l| 4((4))
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||||
4 -->|o| 5((5))
|
||||
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
|
||||
style D fill:#90EE90
|
||||
style F fill:#FFC0CB
|
||||
```
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||||
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||||
---
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||||
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||||
## Repetition: Zero or More
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||||
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||||
`TTA*TT` matches:
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||||
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||||
- "TTTT", "TTATT", "TTAAATT", ...
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||||
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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))
|
||||
style D fill:#90EE90
|
||||
style F fill:#FFC0CB
|
||||
```
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||||
|
||||
---
|
||||
|
||||
## Repetition: One or More
|
||||
|
||||
`TTA+TT` matches:
|
||||
|
||||
- "TTATT", "TTAATT", "TTAAATT", ...
|
||||
- But NOT "TTTT"
|
||||
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||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|T| 1((1))
|
||||
1 -->|T| 2((2))
|
||||
2 -->|A| 3((3))
|
||||
3 -->|A| 3
|
||||
3 -->|T| 4((4))
|
||||
4 -->|T| F((F))
|
||||
style D fill:#90EE90
|
||||
style F fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Exact Repetition
|
||||
|
||||
`A{3,5}` matches:
|
||||
|
||||
- "AAA", "AAAA", "AAAAA"
|
||||
|
||||
`A{3}` matches exactly "AAA"
|
||||
|
||||
---
|
||||
|
||||
## Special Characters
|
||||
|
||||
- `^` - Start of line
|
||||
- `$` - End of line
|
||||
- `\n` - Newline
|
||||
- `\t` - Tab
|
||||
|
||||
Examples:
|
||||
|
||||
- `^start` - "start" at beginning of line
|
||||
- `end$` - "end" at end of line
|
||||
- `^exact$` - "exact" as entire line
|
||||
|
||||
---
|
||||
|
||||
## Alternation
|
||||
|
||||
`papa|mama` matches either:
|
||||
|
||||
- "papa" OR "mama"
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|p| 1((1))
|
||||
1 -->|a| 2((2))
|
||||
2 -->|p| 3((3))
|
||||
3 -->|a| F1((F))
|
||||
|
||||
D -->|m| 4((4))
|
||||
4 -->|a| 5((5))
|
||||
5 -->|m| 6((6))
|
||||
6 -->|a| F2((F))
|
||||
|
||||
style D fill:#90EE90
|
||||
style F1 fill:#FFC0CB
|
||||
style F2 fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Grouping
|
||||
|
||||
`T(AA|AG|GA)` matches:
|
||||
|
||||
- "TAA", "TAG", "TGA"
|
||||
|
||||
Instead of incorrect: `TAA|AG|GA`
|
||||
|
||||
---
|
||||
|
||||
## Backreferences
|
||||
|
||||
`([ACGT]{3})\1{9,}` matches:
|
||||
|
||||
- Any triplet repeated 10+ times
|
||||
- Example: "CAGCAGCAGCAG..."
|
||||
|
||||
---
|
||||
|
||||
## Quick Reference
|
||||
|
||||
### Symbol Ambiguity
|
||||
| Pattern | Matches |
|
||||
|---------|---------|
|
||||
| `.` | Any character |
|
||||
| `[abc]` | a, b, or c |
|
||||
| `[^abc]` | Not a, b, or c |
|
||||
|
||||
### Repetition
|
||||
| Pattern | Matches |
|
||||
|---------|---------|
|
||||
| `?` | 0 or 1 |
|
||||
| `*` | 0 or more |
|
||||
| `+` | 1 or more |
|
||||
| `{n,m}` | n to m times |
|
||||
|
||||
---
|
||||
|
||||
## Biological Application: Gene Finding
|
||||
|
||||
Find Coding Sequences (CDS) in bacterial DNA:
|
||||
|
||||
1. Start codon
|
||||
2. Multiple non-stop codons
|
||||
3. Stop codon
|
||||
|
||||
---
|
||||
|
||||
## Start Codons
|
||||
|
||||
Bacterial start: ATG, TTG, GTG
|
||||
|
||||
Pattern: `[ATG]TG`
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|A/T/G| 1((1))
|
||||
1 -->|T| 2((2))
|
||||
2 -->|G| F((F))
|
||||
style D fill:#90EE90
|
||||
style F fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Stop Codons
|
||||
|
||||
Bacterial stop: TAA, TAG, TGA
|
||||
|
||||
Pattern: `T(A[AG]|GA)`
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|T| 1((1))
|
||||
1 -->|A| 2((2))
|
||||
2 -->|A/G| F1((F))
|
||||
1 -->|G| 3((3))
|
||||
3 -->|A| F2((F))
|
||||
style D fill:#90EE90
|
||||
style F1 fill:#FFC0CB
|
||||
style F2 fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Non-Stop Codons
|
||||
|
||||
61 codons that aren't stop codons
|
||||
|
||||
Pattern: `[ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT])`
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|A/C/G| A1((1))
|
||||
A1 -->|A/C/G/T| A2((2))
|
||||
A2 -->|A/C/G/T| F1((F))
|
||||
D -->|T| B1((3))
|
||||
B1 -->|C/T| B2a((4))
|
||||
B2a -->|A/C/G/T| F2((F))
|
||||
B1 -->|G| B2b((5))
|
||||
B2b -->|C/G/T| F3((F))
|
||||
B1 -->|A| B2c((6))
|
||||
B2c -->|C/T| F4((F))
|
||||
style D fill:#90EE90
|
||||
style F1 fill:#FFC0CB
|
||||
style F2 fill:#FFC0CB
|
||||
style F3 fill:#FFC0CB
|
||||
style F4 fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Complete CDS Pattern
|
||||
|
||||
`[ATG]TG([ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT]))+T(A[GA]|GA)`
|
||||
|
||||
- Start codon
|
||||
- 1+ non-stop codons
|
||||
- Stop codon
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
D((D)) -->|A/T/G| 1((1))
|
||||
1 -->|T| 2((2))
|
||||
2 -->|G| 3((3))
|
||||
3 --> 4((4))
|
||||
4 -->|A/C/G| 5((5))
|
||||
5 -->|A/C/G/T| 6((6))
|
||||
6 -->|A/C/G/T| 7((7))
|
||||
4 -->|T| 8((8))
|
||||
8 -->|C/T| 9((9))
|
||||
9 -->|A/C/G/T| 7
|
||||
8 -->|G| 10((10))
|
||||
10 -->|C/G/T| 7
|
||||
8 -->|A| 11((11))
|
||||
11 -->|C/T| 7
|
||||
7 --> 4
|
||||
7 -->|T| 12((12))
|
||||
12 -->|A| 13((13))
|
||||
13 -->|A/G| F((F))
|
||||
12 -->|G| 14((14))
|
||||
14 -->|A| F
|
||||
style D fill:#90EE90
|
||||
style F fill:#FFC0CB
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Minimum Length CDS
|
||||
|
||||
`[ATG]TG([ACG][ACGT][ACGT]|T([CT][ACGT]|G[CGT]|A[CT])){99,}T(A[GA]|GA)`
|
||||
|
||||
Requires at least 100 amino acids (99 non-stop codons + stop)
|
||||
|
||||
---
|
||||
|
||||
## Summary
|
||||
|
||||
- Regular expressions = text patterns
|
||||
- Symbol ambiguity: `.`, `[]`, `[^]`
|
||||
- Repetition: `?`, `*`, `+`, `{}`
|
||||
- Special chars: `^`, `$`, `\n`, `\t`
|
||||
- Powerful for biological sequence analysis
|
||||
148
web_src/05_Lectures/00_Computers/unix/commande-tube.svg
Normal file
148
web_src/05_Lectures/00_Computers/unix/commande-tube.svg
Normal file
@@ -0,0 +1,148 @@
|
||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
|
||||
<svg width="100%" height="100%" viewBox="0 0 520 73" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;">
|
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<g id="Calque-1" serif:id="Calque 1" transform="matrix(0.338388,0,0,0.338388,6.658634,-44.799997)">
|
||||
<g id="Plan-de-travail1" serif:id="Plan de travail1" transform="matrix(12.595896,0,0,2.955191,-7740.961754,-1114.698045)">
|
||||
<rect x="613" y="422" width="122" height="73" style="fill:none;"/>
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<g transform="matrix(1,0,0,1,-0.234615,0)">
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<g id="text3410-4" transform="matrix(0.085357,0,0,0.363816,611.32066,369.428742)">
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<g transform="matrix(1,0,0,1,739.95099,305.45532)">
|
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<g transform="matrix(17.731146,0,0,17.731146,83.21864,0)">
|
||||
</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">command 2</text>
|
||||
</g>
|
||||
</g>
|
||||
<g id="text3414-7" transform="matrix(0.085357,0,0,0.363816,610.851429,369.428742)">
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<g transform="matrix(1,0,0,1,877.74036,305.45532)">
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<g transform="matrix(17.731146,0,0,17.731146,52.215108,0)">
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</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">options</text>
|
||||
</g>
|
||||
</g>
|
||||
<g id="text3418-2" transform="matrix(0.085357,0,0,0.363816,610.382198,369.428742)">
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<g transform="matrix(1,0,0,1,1039.2732,305.45532)">
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||||
<g transform="matrix(17.731146,0,0,17.731146,73.539235,0)">
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</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">ar<tspan x="13.454px 22.32px " y="0px 0px ">gu</tspan>ments</text>
|
||||
</g>
|
||||
</g>
|
||||
<g id="text3422-2" transform="matrix(0.085357,0,0,0.363816,610.382198,369.428742)">
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<g transform="matrix(1,0,0,1,1246.8026,305.45532)">
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||||
<g transform="matrix(17.731146,0,0,17.731146,83.694818,0)">
|
||||
</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">redirections</text>
|
||||
</g>
|
||||
</g>
|
||||
<g transform="matrix(0.085357,0,0,0.363816,614.37066,369.428742)">
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<g id="text3410" transform="matrix(1,0,0,1,23.641528,0)">
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<g transform="matrix(1,0,0,1,7.861387,305.45532)">
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<g transform="matrix(19.240499,0,0,19.240499,90.302574,0)">
|
||||
</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:19.24px;">command 1</text>
|
||||
</g>
|
||||
</g>
|
||||
<g id="text3414">
|
||||
<g transform="matrix(1,0,0,1,155.65079,305.45532)">
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<g transform="matrix(17.731146,0,0,17.731146,52.215108,0)">
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</g>
|
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<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">options</text>
|
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|
||||
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|
||||
<g id="text3418">
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||||
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<g transform="matrix(17.731146,0,0,17.731146,73.539235,0)">
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</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">ar<tspan x="13.454px 22.32px " y="0px 0px ">gu</tspan>ments</text>
|
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</g>
|
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</g>
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<g id="text3422">
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||||
<g transform="matrix(1,0,0,1,524.71301,305.45532)">
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||||
<g transform="matrix(17.731146,0,0,17.731146,83.694818,0)">
|
||||
</g>
|
||||
<text x="0px" y="0px" style="font-family:'TimesNewRomanPSMT', 'Times New Roman', serif;font-size:17.731px;">redirections</text>
|
||||
</g>
|
||||
</g>
|
||||
</g>
|
||||
</g>
|
||||
</g>
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<g id="rect2575-9" transform="matrix(1,0,0,1.060913,-0,-15.062179)">
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<g transform="matrix(0.674811,0,0,1,42.776636,0)">
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||||
<g transform="matrix(12,0,0,12,195.080696,211.824152)">
|
||||
</g>
|
||||
<text x="131.544px" y="211.824px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">-i -text</text>
|
||||
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|
||||
</g>
|
||||
</g>
|
||||
<g id="rect2575-9-8" transform="matrix(1,0,0,1.060913,-0,-15.062179)">
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<g transform="matrix(0.674811,0,0,1,94.614922,0)">
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||||
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|
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<text x="290.953px" y="211.991px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">pattern</text>
|
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|
||||
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|
||||
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<g transform="matrix(2.955191,0,0,2.785516,-65.010532,-354.886201)">
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||||
<g transform="matrix(0.674811,0,0,1,11.710337,0)">
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<g transform="matrix(12,0,0,12,72.016671,211.666702)">
|
||||
</g>
|
||||
<text x="36.011px" y="211.667px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">egrep</text>
|
||||
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|
||||
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|
||||
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|
||||
<g id="rect2575-9-8-2" transform="matrix(1,0,0,1.060913,-0,-15.062179)">
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|
||||
<text x="497.062px" y="212.017px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">< my_data</text>
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|
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<g id="text9483">
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<g transform="matrix(1,0,0,1,711.88123,272.16415)">
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<g id="rect2575-9-87" transform="matrix(1,0,0,1.060913,0,-15.062179)">
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<g transform="matrix(2.955191,0,0,2.785516,-1661.328781,-355.324777)">
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||||
<g transform="matrix(12,0,0,12,880.2722,211.824152)">
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||||
</g>
|
||||
<text x="865.87px" y="211.824px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">-l</text>
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|
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<g transform="matrix(12,0,0,12,777.450109,211.666702)">
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||||
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|
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<g transform="matrix(12,0,0,12,1292.226228,212.017297)">
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</g>
|
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<text x="1205.812px" y="212.017px" style="font-family:'AndaleMono', 'Andale Mono', monospace;font-size:12px;">> my_results</text>
|
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|
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</g>
|
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<g id="text2571-1">
|
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</g>
|
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<g id="text3410-3">
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<g transform="matrix(1,0,0,1,579.78821,151.48306)">
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<text x="0px" y="0px" style="font-family:'Helvetica';font-size:24px;">tube de jonction stdout > stdin</text>
|
||||
</g>
|
||||
</g>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 9.6 KiB |
167
web_src/05_Lectures/00_Computers/unix/commande.svg
Normal file
167
web_src/05_Lectures/00_Computers/unix/commande.svg
Normal file
@@ -0,0 +1,167 @@
|
||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
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463
web_src/05_Lectures/00_Computers/unix/slides.qmd
Normal file
463
web_src/05_Lectures/00_Computers/unix/slides.qmd
Normal file
@@ -0,0 +1,463 @@
|
||||
|
||||
---
|
||||
title: |
|
||||
DNA metabarcoding School
|
||||
Unix Basics
|
||||
author: frederic.boyer@univ-grenoble-alpes.fr
|
||||
format:
|
||||
revealjs:
|
||||
css: ../../slides.css
|
||||
transition: slide
|
||||
scrollable: true
|
||||
theme: beige
|
||||
html-math-method: mathjax
|
||||
---
|
||||
|
||||
# Introduction to Unix
|
||||
|
||||
|
||||
## Interacting with a UNIX computer
|
||||
|
||||
|
||||
### The command shell endless loop
|
||||
|
||||
{ width=80% }
|
||||
|
||||
|
||||
|
||||
## Bash
|
||||
|
||||
The basic command interpreter on the machine (and most often found on a linux machine) is `bash`.
|
||||
|
||||
|
||||
> Bash is a command processor that typically runs in a text window, where the user types commands that cause actions. Bash can also read commands from a file, called a script. Like all Unix shells, it supports filename globbing (wildcard matching), piping, here documents, command substitution, variables and control structures for condition-testing and iteration. The keywords, syntax and other basic features of the language were all copied from sh. Other features, e.g., history, were copied from csh and ksh. Bash is a POSIX shell, but with a number of extensions.
|
||||
>
|
||||
> [wikipedia:bash](https://en.wikipedia.org/wiki/Bash_%28Unix_shell%29)
|
||||
|
||||
|
||||
## RTFM !
|
||||
|
||||
> RTFM is an initialism for the expression "read the fucking manual" or, in the context of the Unix computer operating system, "read the fucking man page". The RTFM comment is usually expressed when the speaker is irritated by another person's question or lack of knowledge. It refers to either that person's inability to read a technical manual, or to their perceived laziness in not doing so first, before asking the question.
|
||||
>
|
||||
> [wikipedia:RTFM](https://en.wikipedia.org/wiki/RTFM)
|
||||
|
||||
|
||||
The official `bash` documentation: [documentation]( https://www.gnu.org/software/bash/manual/ )
|
||||
|
||||
|
||||
## RTFM: getting help with `man`
|
||||
|
||||
> A man page (short for manual page) is a form of software documentation usually found on a Unix or Unix-like operating system. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts. A user may invoke a man page by issuing the man command.
|
||||
>
|
||||
> [wikipedia:man page](https://en.wikipedia.org/wiki/Man_page)
|
||||
|
||||
| Useful command | What it does |
|
||||
|----------------------|-----------------------------------------|
|
||||
| `man <command>` | prints manual for the `command` command |
|
||||
|
||||
For example, to get the manual page for the `man` command:
|
||||
|
||||
```bash
|
||||
man man
|
||||
```
|
||||
|
||||
## RTFM: getting help with `-h` or `--help`
|
||||
|
||||
When there is no man page associated to a command one can use the `-h` or `--help` options:
|
||||
|
||||
For example, to get the help associated to the `man` command:
|
||||
|
||||
```bash
|
||||
man --help
|
||||
```
|
||||
|
||||
# Filesystem -- basic commands and streams
|
||||
|
||||
{ width=40% }
|
||||
|
||||
## Absolute path
|
||||
|
||||
> An absolute or full path points to the same location in a file system, regardless of the current working directory. To do that, it must include the root directory.
|
||||
>
|
||||
> [wikipedia:Path(computing)](https://en.wikipedia.org/wiki/Path_(computing))
|
||||
|
||||
The root of the filesystem is designed by `/`.
|
||||
|
||||
The different part of the path are separated by `/`.
|
||||
|
||||
## Absolute path
|
||||
|
||||
|
||||
{ width=30% }
|
||||
|
||||
The red path is : `/etc/passwd`
|
||||
|
||||
## Relative path
|
||||
|
||||
> By contrast, a relative path starts from some given working directory, avoiding the need to provide the full absolute path.
|
||||
>
|
||||
> [wikipedia:Path (computing)]( https://en.wikipedia.org/wiki/Path_(computing) )
|
||||
|
||||
## Special directories :
|
||||
- `~` : *home directory* for the current user
|
||||
- `~name` : *home directory* for user *name*
|
||||
- `.` : Current directory
|
||||
- `..` : Parent directory
|
||||
|
||||
{ width=30% }
|
||||
|
||||
|
||||
## Useful commands to interact with the filesystem
|
||||
|
||||
| Useful commands | What it does |
|
||||
|----------------------------|-----------------------------|
|
||||
| `pwd` | print working directory |
|
||||
| `cd <directory>` | change directory |
|
||||
| `mkdir <filename>` | create directory |
|
||||
| `ls <filename>` | list files and directories |
|
||||
| `touch <filename>` | create or touch a file |
|
||||
| `cp <filename> <filename>` | copy files or directories |
|
||||
| `mv <filename> <filename>` | move files or directories |
|
||||
| `rm <filename>` | remove files or directories |
|
||||
|
||||
|
||||
## Permissions
|
||||
|
||||
Files and directories are assigned permissions or access rights to specific users and groups of users. The permissions control the ability of the users to view, change, navigate, and execute the contents of the file system.
|
||||
|
||||
> Permissions on Unix-like systems are managed in three distinct scopes or classes.
|
||||
> These scopes are known as user, group, and others.
|
||||
>
|
||||
> [wikipedia: unix permissions](https://en.wikipedia.org/wiki/File_system_permissions#Traditional_Unix_permissions)
|
||||
|
||||
## Permissions
|
||||
|
||||
{ width=10% }
|
||||
|
||||
> The modes indicate which permissions are to be granted or taken away from the specified classes.
|
||||
> There are three basic modes which correspond to the basic permissions:
|
||||
>
|
||||
> | Mode | Name | Description |
|
||||
> |------|---------|--------------------------------------------|
|
||||
> | r | read | read a file or list a directory's contents |
|
||||
> | w | write | write to a file or directory |
|
||||
> | x | execute | execute a file or recurse a directory tree |
|
||||
>
|
||||
> [wikipedia:modes](https://en.wikipedia.org/wiki/Modes_(Unix))
|
||||
|
||||
## View and change permissions
|
||||
|
||||
| Useful commands | What it does |
|
||||
|------------------------------|--------------------|
|
||||
| `ls -l` | view permissions |
|
||||
| `chmod <options> <filename>` | change permissions |
|
||||
|
||||
|
||||
## For example:
|
||||
|
||||
```bash
|
||||
fboyer@obitools:~/$ ls -l index.html
|
||||
-rw-rw-r-- 1 fboyer fboyer 3101 déc. 21 17:09 index.html
|
||||
fboyer@obitools:~/$ chmod 500 index.html
|
||||
fboyer@obitools:~/$ ls -l index.html
|
||||
-r-x------ 1 fboyer fboyer 3101 déc. 21 17:09 index.html
|
||||
```
|
||||
|
||||
|
||||
|
||||
# Commands to work with text
|
||||
|
||||
## Visualize the content of a file
|
||||
|
||||
| Useful commands | What it does |
|
||||
|--------------------|----------------------------------------|
|
||||
| `less <filename>` | utility to explore text files |
|
||||
|
||||
|
||||
## The `less` command
|
||||
|
||||
| shortcut | What it does |
|
||||
|-----------------------|-------------------------------------------|
|
||||
| `h` | display help |
|
||||
| `q` | quit |
|
||||
| `/` | search for a regular pattern |
|
||||
| `n` | for the Next occurence of the pattern |
|
||||
| `shift-n` | for the previous occurence of the pattern |
|
||||
| `arrows` and `space` | to navigate |
|
||||
| `g` and `G` | go to top and end of the file |
|
||||
|
||||
## Edit a text file
|
||||
|
||||
| Useful commands | What it does |
|
||||
|--------------------|--------------------|
|
||||
| `nano <filename>` | Simple text editor |
|
||||
|
||||
|
||||
{ width=100% }
|
||||
|
||||
## Basic `Unix` commands to manipulate text files
|
||||
|
||||
| Useful commands | What it does |
|
||||
|-------------------------------|------------------------------------------------------------------|
|
||||
| `cat <filename>` | output the content of `filename` file |
|
||||
| `head [-<N>] <filename>` | output the first `N` lines of `filename` |
|
||||
| `tail [-<N>] <filename>` | output the last `N` lines of `filename` |
|
||||
| `sort [options] <filename>` | sort the content of `filename` and output it |
|
||||
| `cut [options] <filename>` | extract some column from `filename` and output it |
|
||||
| `diff [options] <filenames>` | compare files line by line and output the differences |
|
||||
|
||||
## Basic `Unix` commands to manipulate text files
|
||||
|
||||
| Useful commands | What it does |
|
||||
|-------------------------------|------------------------------------------------------------------|
|
||||
| `join [options] <filename> <filename>` | join files on the basis of column content |
|
||||
| `paste [options] <filenames>` | paste files line by line |
|
||||
| `wc [options] <filenames>` | count characters, words or lines |
|
||||
| `find <directory> [options]` | search files (Ex: `find . -name '*.txt'`) |
|
||||
| `sed <command> <filename>` | process file line by line for basic editing |
|
||||
| `grep [options] <regular expression> <filenames>` | search files for a *pattern* |
|
||||
| `egrep [options] <extended regular expression> <filenames>` | similar as using the `-e` option of `grep` |
|
||||
|
||||
## `Unix` streams
|
||||
|
||||
> In computer programming, standard streams are pre-connected input and output channels that allow communication between a computer program and its environment when the program begins execution.
|
||||
> The three I/O connections are called standard input (`stdin`), standard output (`stdout`) and standard error (`stderr`).
|
||||
|
||||
A basic `Unix` command: Piping a stream into another command> [wikipedia:streams](https://en.wikipedia.org/wiki/Standard_streams)
|
||||
|
||||
## A basic `Unix` command
|
||||
|
||||
{ width=50% }
|
||||
|
||||
standard input (`stdin`), standard output (`stdout`), standard error (`stderr`) and parameters don't need to be specified.
|
||||
|
||||
By default, `stdin` is empty, `stdout` and `stderr` output their content to the terminal.
|
||||
|
||||
## A basic `Unix` command: Specifying parameters
|
||||
|
||||
#### Exemples: Parameters
|
||||
|
||||
```bash
|
||||
grep -B 2 root /etc/passwd
|
||||
```
|
||||
|
||||
{ width=60% }
|
||||
|
||||
## A basic `Unix` command: Sending the content of a text file to the standard input
|
||||
|
||||
Most of the commands that handle text can, if no file is given as a parameter, use the content of `stdin`.
|
||||
|
||||
#### Exemples: Redirecting the standard input
|
||||
|
||||
```bash
|
||||
grep -B 2 root < /etc/passwd
|
||||
```
|
||||
|
||||
{ width=40% }
|
||||
|
||||
## A basic `Unix` command: Creating a text file from the output of a command
|
||||
|
||||
### Exemples: Redirecting the standard output
|
||||
|
||||
```bash
|
||||
# > create or replace file
|
||||
# >> append to file
|
||||
grep -B 2 root < /etc/passwd > result
|
||||
```
|
||||
|
||||
{width = 40%}
|
||||
|
||||
## A basic `Unix` command: Piping a stream into another command
|
||||
|
||||
### Exemples: Redirecting the standard output
|
||||
|
||||
```bash
|
||||
# > create or replace file
|
||||
# >> append to file
|
||||
grep -B 2 root < /etc/passwd | less
|
||||
```
|
||||
|
||||
{width = 20%}
|
||||
|
||||
## RTFM: Bash redirections
|
||||
|
||||
[Bash redirections](https://www.gnu.org/software/bash/manual/html_node/Redirections.html)
|
||||
|
||||
# The bash command challenge !
|
||||
|
||||
|
||||
{ width=80% }
|
||||
|
||||
|
||||
[I accept the challenge !](https://cmdchallenge.com/)
|
||||
|
||||
|
||||
|
||||
# The `OBITools`
|
||||
|
||||
{width = 80%}
|
||||
|
||||
## RTFM !
|
||||
|
||||
The [documentation](http://obitools4.metabarcoding.org) is available online.
|
||||
|
||||
{width = 80%}
|
||||
|
||||
## An `OBITools` command
|
||||
|
||||
{width = 80%}
|
||||
|
||||
|
||||
## Decorated fasta sequences
|
||||
|
||||
Basic fasta sequence:
|
||||
|
||||
```
|
||||
>my_sequence this is my pretty sequence
|
||||
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||
AACGACGTTGCAGTACGTTGCAGT
|
||||
```
|
||||
|
||||
*Decorated* fasta sequence:
|
||||
|
||||
```
|
||||
>my_sequence taxid=3456; direct=True; sample=A354; this is my pretty sequence
|
||||
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||
AACGACGTTGCAGTACGTTGCAGT
|
||||
```
|
||||
*decoration* can be any set of `key=value;` couples
|
||||
|
||||
## Main OBITools commands (1/2)
|
||||
|
||||
|
||||
- Metabarcode design and quality assessment
|
||||
- `ecoPCR`: in silico PCR
|
||||
- `ecoPrimers`: new barcode markers and primers
|
||||
- `ecotaxstat`: getting the coverage of an ecoPCR output compared to the original ecoPCR database
|
||||
- `ecotaxspecificity`: Evaluates barcode resolution
|
||||
|
||||
- File format conversions
|
||||
- `obiconvert`: converts sequence files to different output formats
|
||||
- `obitab`: converts a sequence file to a tabular file
|
||||
|
||||
- Sequence annotations
|
||||
- `ecotag`: assigns sequences to taxa
|
||||
- `obiannotate`: adds/edits sequence record annotations
|
||||
|
||||
## Main OBITools commands (2/2)
|
||||
|
||||
- Computations on sequences
|
||||
- `illuminapairedend`: aligns paired-end Illumina reads
|
||||
- `ngsfilter`: Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
|
||||
- `obiclean`: tags a set of sequences for PCR/sequencing errors identification
|
||||
- `obiuniq`: groups and dereplicates sequences
|
||||
|
||||
- Sequence sampling and filtering
|
||||
- `obigrep`: filters sequence file
|
||||
- `obihead`: extracts the first sequence records
|
||||
|
||||
- Statistics over sequence file
|
||||
- `obicount`: counts the number of sequence records
|
||||
- `obistat`: computes basic statistics for attribute values
|
||||
|
||||
|
||||
## Regular expressions: Regex
|
||||
|
||||
> In computing, a regular expression is a specific pattern that provides concise and flexible means to "match" (specify and recognize) strings of text, such as particular characters, words, or patterns of characters.
|
||||
>
|
||||
> Common abbreviations for "regular expression" include regex and regexp.
|
||||
> - http://en.wikipedia.org/wiki/Regular_expression
|
||||
|
||||
## Graphical representation
|
||||
|
||||
A regular expression can be represented by an *automata*
|
||||
|
||||
{ width=50% }
|
||||
|
||||
## Occurrence of a regular pattern
|
||||
|
||||
If one can get to the final state, the text `match` the regular expression.
|
||||
|
||||
|
||||
{ width=50% }
|
||||
|
||||
> Tutu et **_toto_** sont sur un bateau. Toto tombe à l’eau.
|
||||
|
||||
> Obama: «If daughters get tat**_too_**s, we will **_too_**»
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `ATG` (start codon) | { width=100% } |
|
||||
| `[ATG]TG` <br> `[^C]TG`(all start codons) | ![[ATG]TG](images/exp3.svg){ width=100% } |
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `.TG` <br> `[ACGT]TG` (all codons ending with TG) | { width=100% } |
|
||||
| `TTA+TT` <br> `TTAA*TT` (TT, at least one A, TT) | { width=100% } |
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `TAA`|`TAG`|`TGA` <br> `T(AA`|`AG`|`GA)` (All stop codons) | { width=100% } |
|
||||
|
||||
## Syntax of regular expressions
|
||||
|
||||
| Syntax | What it matches |
|
||||
|-------------------|--------------------------------------------------|
|
||||
| `^` | begining of the line |
|
||||
| `$` | end of the line |
|
||||
| `[]` | set of characters |
|
||||
| `[^]` | all characters but these ones (ex: `TTA{3,5}TT`) |
|
||||
| | | multiple choices |
|
||||
| `{}` | repetitions |
|
||||
| `*` | any number of times |
|
||||
| `+` | at least once |
|
||||
| `?` | none or once |
|
||||
| `\*` | the `*` character (same for `+`, `(`, `[`, ...) |
|
||||
|
||||
## Special characters: Regular expression extensions
|
||||
|
||||
| Special characters| What it matches |
|
||||
|-------------------|--------------------------------------------------|
|
||||
| `()` | used to define sub-expressions |
|
||||
| `\n` | used to reuse the text matched by the `n`th sub-expression |
|
||||
|
||||
## Syntax of extended regular expressions
|
||||
|
||||
Extended regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `([ACGT]{3})\1{9,}` (matching a stretch of at least the same codon 10 times) | As the langage described is not regular, no automaton can be used to represent the expression |
|
||||
|
||||
|
||||
[What is my regular expression engine capable of ?](https://en.wikipedia.org/wiki/Comparison_of_regular_expression_engines)
|
||||
|
||||
## Regular expressions and `obigrep`
|
||||
|
||||
Regular expressions can be used with `obigrep` to filter sequences with the appropriate options:
|
||||
|
||||
-s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>
|
||||
regular expression pattern used to select the
|
||||
sequence. The pattern is case insensitive
|
||||
-D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>
|
||||
regular expression pattern matched against the
|
||||
definition of the sequence. The pattern is case
|
||||
sensitive
|
||||
-I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>
|
||||
regular expression pattern matched against the
|
||||
identifier of the sequence. The pattern is case
|
||||
sensitive
|
||||
975
web_src/05_Lectures/00_Computers/unix/unix-modern-bash.qmd
Normal file
975
web_src/05_Lectures/00_Computers/unix/unix-modern-bash.qmd
Normal file
@@ -0,0 +1,975 @@
|
||||
---
|
||||
title: "Introduction to Unix by Example"
|
||||
subtitle: "A Modern Approach for Bioinformaticians"
|
||||
author: "Updated Course Material"
|
||||
date: today
|
||||
format:
|
||||
html:
|
||||
toc: true
|
||||
toc-depth: 3
|
||||
number-sections: true
|
||||
code-fold: false
|
||||
theme: cosmo
|
||||
---
|
||||
|
||||
# Why Unix?
|
||||
|
||||
The Unix operating system was born in AT&T laboratories in the United States, then known as "Bell Labs". Created in the late 1960s, it derives from Multics, another system from the same laboratory about ten years earlier. Unix spread rapidly because Bell Labs distributed its new system as freely modifiable source code. This led to the emergence of Unix families produced by the system's main users: research laboratories on one hand and major computer manufacturers on the other.
|
||||
|
||||
From the beginning, Unix development has been closely linked to scientific computing. These intrinsic qualities explain why this operating system is still widely used in many research fields today.
|
||||
|
||||
Today, Unix is a registered trademark of The Open Group, which standardizes all Unix systems. However, there is a broader definition that includes "Unix-like" systems such as GNU/Linux. Despite proclaiming in its name not to be Unix (GNU is Not Unix), this family of operating systems has such functional similarities with its ancestor that it's difficult to explain how it isn't Unix.
|
||||
|
||||
Nowadays, a Unix system can be installed on virtually any machine, from personal computers to large computing servers. Notably, for several years, Apple's standard operating system on Macintosh computers, macOS, has been a certified Unix system.
|
||||
|
||||
# Unix System Overview
|
||||
|
||||
Unix is a multitasking and multi-user operating system. This means it can manage the simultaneous use of the same computer by multiple people, and for each person, it allows parallel execution of multiple programs. The multiplicity of users and running programs on the same machine requires particular resource management, involving restricted rights for each user so that one person's work doesn't interfere with another's.
|
||||
|
||||
```{mermaid}
|
||||
flowchart TB
|
||||
U1["User 1"] --> S1["Shell<br/>(Command Interpreter)"]
|
||||
U2["User 2"] --> S1
|
||||
U3["User N"] --> S1
|
||||
|
||||
subgraph Unix ["Unix Operating System"]
|
||||
S1["Shell<br/>(Command Interpreter)"] --> K1["Kernel<br/>(Core System)"]
|
||||
K1 --> R1["CPU"]
|
||||
K1 --> R2["Memory"]
|
||||
K1 --> R3["Disk Storage"]
|
||||
K1 --> R4["Network"]
|
||||
end
|
||||
```
|
||||
|
||||
## Users
|
||||
|
||||
Each Unix system user needs an account or "machine access right" to work. Each account is identified by a login name.
|
||||
|
||||
Associated with each login:
|
||||
|
||||
- A password that secures system access
|
||||
- A user ID (UID) that identifies the user on the machine
|
||||
- A location on the hard drive to store user files, called Home directory
|
||||
- A user group, allowing collaborative work (see later)
|
||||
|
||||
Information about all users on a machine is typically stored in a text file: `/etc/passwd`
|
||||
|
||||
```bash
|
||||
root:x:0:0:root:/root:/bin/bash
|
||||
bin:x:1:1:bin:/bin:/sbin/nologin
|
||||
daemon:x:2:2:daemon:/sbin:/sbin/nologin
|
||||
mail:x:8:12:mail:/var/spool/mail:/sbin/nologin
|
||||
alice:x:1000:1000:Alice Smith:/home/alice:/bin/bash
|
||||
bob:x:1001:1001:Bob Jones:/home/bob:/bin/bash
|
||||
```
|
||||
|
||||
Each line corresponds to a user. Information is separated by `:` characters. In order: login, encoded password, UID, group ID, full name, home directory, and default shell.
|
||||
|
||||
## The File System
|
||||
|
||||
The file system of an operating system encompasses all mechanisms for managing storage space (hard drives) on the computer. Data and programs are stored in files. A file can be thought of as a small part of a hard drive dedicated to storing a set of data.
|
||||
|
||||
### File Names
|
||||
|
||||
In a Unix system, a file name describes a path in a tree. A file name starts with a `/` character and consists of successive node labels describing the file's location in the name tree. Each label is separated from the preceding one by the `/` character.
|
||||
|
||||
```{mermaid}
|
||||
graph TB
|
||||
root["/"]
|
||||
root --> bin["/bin"]
|
||||
root --> etc["/etc"]
|
||||
root --> home["/home"]
|
||||
root --> usr["/usr"]
|
||||
root --> var["/var"]
|
||||
|
||||
etc --> passwd["passwd"]
|
||||
etc --> hosts["hosts"]
|
||||
|
||||
home --> alice["alice"]
|
||||
home --> bob["bob"]
|
||||
|
||||
alice --> documents["documents"]
|
||||
alice --> data["data.txt"]
|
||||
|
||||
usr --> local["/local"]
|
||||
usr --> usrbin["/bin"]
|
||||
|
||||
style passwd fill:#e1f5ff
|
||||
style root fill:#ffe1e1
|
||||
```
|
||||
|
||||
For example, the file `/etc/passwd` indicates that this file is located at a node (directory) named `/etc`, which itself is located at the root of the file name tree `/`.
|
||||
|
||||
### Standard Directory Structure
|
||||
|
||||
Certain directories are found in many Unix systems:
|
||||
|
||||
- `/etc` - Contains system configuration files
|
||||
- `/var` - Contains system operation information
|
||||
- `/bin` - Contains basic system programs
|
||||
- `/usr` - Contains a large part of the system
|
||||
- `/usr/local` - Contains programs specific to a machine
|
||||
- `/home` - Contains user home directories
|
||||
- `/tmp` - Temporary files
|
||||
|
||||
### Lexical Rules for File Names
|
||||
|
||||
File name labels can contain:
|
||||
|
||||
- Alphabetic characters (a-z and A-Z)
|
||||
- Numeric characters (0-9)
|
||||
- Punctuation marks (& , $ , * , + , = , . , etc.)
|
||||
|
||||
However, using some of these signs can cause problems. It's recommended to use only: `. , % , - , _ , : , =`
|
||||
|
||||
**Important**: Unix is case-sensitive. `TODO`, `todo`, `Todo`, and `ToTo` are all different names.
|
||||
|
||||
File names starting with a dot `.` are hidden files and typically correspond to configuration files.
|
||||
|
||||
### Links
|
||||
|
||||
The concept of a link can be compared to a shortcut in other operating systems. A link is a special file that creates additional edges in the file name tree. From a computer science perspective, the tree structure becomes a Directed Acyclic Graph (DAG).
|
||||
|
||||
```{mermaid}
|
||||
graph LR
|
||||
root["/"]
|
||||
usr["/usr"]
|
||||
bin["/bin"]
|
||||
home["/home"]
|
||||
alice["alice"]
|
||||
programs["programs<br/>(link)"]
|
||||
grep["grep"]
|
||||
|
||||
root --> usr
|
||||
root --> home
|
||||
usr --> bin
|
||||
home --> alice
|
||||
alice --> programs
|
||||
bin --> grep
|
||||
programs -.->|symbolic link| bin
|
||||
|
||||
style programs fill:#fff2cc
|
||||
style grep fill:#e1f5ff
|
||||
```
|
||||
|
||||
Creating a link in a Unix file system creates a synonym between the link name and the target file.
|
||||
|
||||
### The `.` and `..` Directories
|
||||
|
||||
Unix uses links to facilitate navigation in the file name tree. When creating a directory node, the system automatically adds two links under this node named `.` and `..`:
|
||||
|
||||
- `.` links to the directory containing it
|
||||
- `..` points to the parent directory
|
||||
|
||||
```{mermaid}
|
||||
graph TB
|
||||
root["/"]
|
||||
home["/home"]
|
||||
alice["alice"]
|
||||
dot[". (alice)"]
|
||||
dotdot[".. (home)"]
|
||||
docs["documents"]
|
||||
|
||||
root --> home
|
||||
home --> alice
|
||||
alice --> dot
|
||||
alice --> dotdot
|
||||
alice --> docs
|
||||
|
||||
dot -.-> alice
|
||||
dotdot -.-> home
|
||||
|
||||
style dot fill:#fff2cc
|
||||
style dotdot fill:#fff2cc
|
||||
```
|
||||
|
||||
These links mean that for each file, there isn't just one name but an infinite number of possible names. The file `/home/alice/myfile` can also be named:
|
||||
|
||||
- `/home/alice/./myfile`
|
||||
- `/home/alice/../../home/alice/myfile`
|
||||
- `/home/alice/./././myfile`
|
||||
|
||||
### Current Directory and Relative Paths
|
||||
|
||||
The hierarchical tree structure of Unix file names is powerful but produces often very long file names. To work around this problem, Unix offers the concept of current directory and relative paths.
|
||||
|
||||
**Current Directory**: When working on a machine, you typically work on a set of files located in the same region of the name tree. The common part of all these names is stored in an environment variable called `PWD` (Present Working Directory).
|
||||
|
||||
By default, when you log into your Unix account, this variable is initialized with your home directory name. You can change this variable's value using the `cd` command.
|
||||
|
||||
**Relative Paths**: Relative file names are expressed relative to the current directory. To know the true name corresponding to a relative name, you concatenate the current directory name and the relative name.
|
||||
|
||||
Example:
|
||||
```bash
|
||||
# If current directory is: /home/alice/experiment_1
|
||||
# These files:
|
||||
/home/alice/experiment_1/sequence.fasta
|
||||
/home/alice/experiment_1/expression.dat
|
||||
/home/alice/experiment_1/annotation.gff
|
||||
|
||||
# Can be named simply:
|
||||
sequence.fasta
|
||||
expression.dat
|
||||
annotation.gff
|
||||
```
|
||||
|
||||
A relative name is recognized by the fact it doesn't start with `/`. In contrast, complete file names are called absolute paths and always start with `/`.
|
||||
|
||||
### Access Rights
|
||||
|
||||
Unix is a multi-user system. To protect each user's data from others, each file belongs to a specific user (usually its creator) and a user group. Additionally, each file has access rights concerning:
|
||||
|
||||
- The file owner
|
||||
- The group to which the file belongs
|
||||
- All other system users
|
||||
|
||||
For each of these three user categories, there are read, write, and execute rights:
|
||||
|
||||
- **Read right**: Allows reading the file
|
||||
- **Write right**: Authorizes modifying or deleting the file
|
||||
- **Execute right**: Allows executing the file if it contains a program
|
||||
|
||||
For directories, execute right indicates permission to use it as an element of a file name.
|
||||
|
||||
```bash
|
||||
# Example of file permissions
|
||||
$ ls -l
|
||||
-rw-r--r-- 1 alice staff 1024 Nov 03 10:30 data.txt
|
||||
-rwxr-xr-x 1 alice staff 2048 Nov 03 10:31 script.sh
|
||||
drwxr-xr-x 2 alice staff 512 Nov 03 10:32 results
|
||||
```
|
||||
|
||||
Rights can be modified by the file owner using the `chmod` instruction.
|
||||
|
||||
## Processes
|
||||
|
||||
A program corresponds to a sequence of calculation instructions that the computer must execute to perform a task. While it's important to store this instruction sequence for regular reuse, it's equally important to execute it. A process corresponds to the execution of a program.
|
||||
|
||||
Since Unix is multitasking and multi-user, the same program can be executed simultaneously by multiple processes. It's therefore important to distinguish between program and process.
|
||||
|
||||
### Process Anatomy
|
||||
|
||||
A process can be considered as part of the computer's memory dedicated to program execution. This memory chunk can be divided into three main parts: the environment, data area, and program area.
|
||||
|
||||
```{mermaid}
|
||||
flowchart TB
|
||||
subgraph Process["Process Memory Space"]
|
||||
direction TB
|
||||
Env["Environment<br/>- Variables<br/>- File descriptors<br/>- PID/PPID"]
|
||||
Code["Code Area<br/>- Program instructions"]
|
||||
Data["Data Area<br/>- Variables<br/>- Computation results"]
|
||||
end
|
||||
|
||||
Parent["Parent Process"] -.->|fork| Process
|
||||
|
||||
style Env fill:#e1f5ff
|
||||
style Code fill:#ffe1e1
|
||||
style Data fill:#e1ffe1
|
||||
```
|
||||
|
||||
### Process Environment
|
||||
|
||||
A process is an isolated memory area where a program executes. Isolation secures the computer by preventing a program from corrupting others' execution. However, during execution, a program must interact with the rest of the computer.
|
||||
|
||||
The process environment is dedicated to this interface task. It contains descriptions of system elements the process needs to know. Two main types of information are stored:
|
||||
|
||||
**Environment Variables**: Associate a name with a value describing certain system properties. Examples:
|
||||
|
||||
- `PWD`: Current Working Directory for interpreting relative paths
|
||||
- `PATH`: List of directories where available programs are stored
|
||||
- `HOME`: User's home directory
|
||||
- `USER`: Current username
|
||||
|
||||
**Streams**: Virtual pipes through which data transits. By default, three streams are associated with each process:
|
||||
|
||||
- `stdin` (standard input): How a Unix program normally receives data
|
||||
- `stdout` (standard output): Used by the program to return results
|
||||
- `stderr` (standard error): Used for error messages and information
|
||||
|
||||
```{mermaid}
|
||||
flowchart LR
|
||||
Input[("Input<br/>Source")] --> stdin["stdin<br/>(0)"]
|
||||
stdin --> Process["Process"]
|
||||
Process --> stdout["stdout<br/>(1)"]
|
||||
Process --> stderr["stderr<br/>(2)"]
|
||||
stdout --> Output[("Output<br/>Destination")]
|
||||
stderr --> Error[("Error<br/>Log")]
|
||||
|
||||
style stdin fill:#e1f5ff
|
||||
style stdout fill:#e1ffe1
|
||||
style stderr fill:#ffe1e1
|
||||
```
|
||||
|
||||
### Process Lifecycle
|
||||
|
||||
Every process has a parent (except the initial process) and inherits all its properties: environment, data area, and program code to execute.
|
||||
|
||||
```{mermaid}
|
||||
stateDiagram-v2
|
||||
[*] --> Init: System Boot
|
||||
Init --> Parent: fork()
|
||||
Parent --> Child1: fork()
|
||||
Parent --> Child2: fork()
|
||||
Child1 --> [*]: exit()
|
||||
Child2 --> [*]: exit()
|
||||
Parent --> [*]: All children terminated
|
||||
|
||||
note right of Parent
|
||||
PID: 1234
|
||||
Creates child processes
|
||||
end note
|
||||
|
||||
note right of Child1
|
||||
PID: 1235
|
||||
Inherits parent environment
|
||||
end note
|
||||
```
|
||||
|
||||
Important points:
|
||||
|
||||
- Every process has a parent and inherits all its properties
|
||||
- A child process must terminate before its parent
|
||||
- When you close your shell, all running programs are terminated unless detached
|
||||
- A process is created by copying its parent, inheriting its properties except PID
|
||||
|
||||
The normal chronology for creating a new process:
|
||||
|
||||
1. Call the `fork()` function
|
||||
2. Test which process continues execution
|
||||
3. In the child process, call `exec()` to replace the program code
|
||||
4. At execution end, notify the parent and wait for cleanup
|
||||
|
||||
# The Unix Shell - A Working Environment
|
||||
|
||||
The Unix shell is the most important program for a Unix user. It's how they interact with their computer. There's a graphical window system under Unix similar to Windows or macOS, called X Window System (X11), which can operate in client/server mode across networks. However, we'll focus on interacting with Unix in "text" mode via the shell.
|
||||
|
||||
The Unix shell is a program capable of interpreting a command language. These commands allow users to launch program execution by specifying:
|
||||
|
||||
- Data to work on
|
||||
- Parameters to adjust execution
|
||||
- What to do with results
|
||||
|
||||
Several Unix shells exist, differing mainly in their command language syntax. The two most commonly used today are:
|
||||
|
||||
- **bash** (Bourne Again Shell): Modern version of the Bourne shell (sh)
|
||||
- **zsh** (Z Shell): Enhanced version with additional features
|
||||
|
||||
This course focuses on **bash**, the default shell on most Linux systems and macOS.
|
||||
|
||||
## Basic Command Structure
|
||||
|
||||
A shell command describes how to trigger program execution with all necessary information. As a principle, every program installed on a Unix machine corresponds to a usable command from the shell bearing the program's name, and conversely, every Unix command is the name of an installed program.
|
||||
|
||||
```{mermaid}
|
||||
flowchart LR
|
||||
Command["Command<br/>(program name)"] --> Options["Options<br/>(flags)"]
|
||||
Options --> Arguments["Arguments<br/>(input files)"]
|
||||
Arguments --> Redirection["I/O Redirection<br/>(< > |)"]
|
||||
|
||||
style Command fill:#ffe1e1
|
||||
style Options fill:#e1f5ff
|
||||
style Arguments fill:#e1ffe1
|
||||
style Redirection fill:#fff2cc
|
||||
```
|
||||
|
||||
A Unix command line has four main parts:
|
||||
|
||||
1. **Command** (required): Program name
|
||||
2. **Options** (optional): Adjust program behavior
|
||||
3. **Arguments** (optional): Specify data to process
|
||||
4. **Redirection** (optional): Control input/output
|
||||
|
||||
### The Unix Command
|
||||
|
||||
A Unix command is the name of a program installed on the machine. When you execute a command like `ls` or `grep`, you're actually launching execution of an eponymous program stored somewhere on your hard drives.
|
||||
|
||||
The machine searches for program files only in a subset of existing directories, described by a list stored in the `PATH` environment variable.
|
||||
|
||||
```bash
|
||||
$ echo $PATH
|
||||
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
|
||||
```
|
||||
|
||||
Directories are searched in order. If programs with the same name exist in different directories, the first one found is executed.
|
||||
|
||||
To execute a program in a directory not listed in `PATH`, specify its location:
|
||||
|
||||
```bash
|
||||
# Using absolute path
|
||||
$ /home/alice/myprograms/myscript.sh
|
||||
|
||||
# Using relative path (if in the directory)
|
||||
$ ./myscript.sh
|
||||
```
|
||||
|
||||
The `./` prefix is necessary to indicate the current directory location.
|
||||
|
||||
### Command Options
|
||||
|
||||
Options alter command functionality by adjusting parameters. Options are recognizable as:
|
||||
|
||||
- Short form: Single character preceded by `-` (e.g., `-l`)
|
||||
- Long form: Complete word preceded by `--` (e.g., `--list`)
|
||||
|
||||
Many programs offer both forms for the same option.
|
||||
|
||||
```bash
|
||||
# Short option
|
||||
$ grep -i root /etc/passwd
|
||||
|
||||
# Long option (equivalent)
|
||||
$ grep --ignore-case root /etc/passwd
|
||||
```
|
||||
|
||||
Some options require arguments:
|
||||
|
||||
```bash
|
||||
# Short form with argument
|
||||
$ grep -B 2 root /etc/passwd
|
||||
$ grep -B2 root /etc/passwd # No space also works
|
||||
|
||||
# Long form with argument
|
||||
$ grep --before-context=2 root /etc/passwd
|
||||
```
|
||||
|
||||
Multiple short options can be combined:
|
||||
|
||||
```bash
|
||||
# Separate options
|
||||
$ grep -i -n root /etc/passwd
|
||||
|
||||
# Combined options
|
||||
$ grep -in root /etc/passwd
|
||||
```
|
||||
|
||||
If an option requires an argument, it must be placed last in the group.
|
||||
|
||||
### Command Arguments
|
||||
|
||||
Arguments indicate data the program should process, beyond data potentially transmitted through standard input. Depending on how it's programmed, a program can accept one or multiple arguments. Each argument may have a distinct role depending on the program.
|
||||
|
||||
To understand each argument's role, consult the program's manual page via `man` command or online help, usually accessible with the `-h` option.
|
||||
|
||||
```bash
|
||||
# Example with multiple arguments
|
||||
$ cp source.txt destination.txt
|
||||
|
||||
# Example with patterns
|
||||
$ grep "pattern" file1.txt file2.txt file3.txt
|
||||
```
|
||||
|
||||
### I/O Redirection Instructions
|
||||
|
||||
This fourth part of a Unix command line is crucial, allowing you to specify how your program should configure its standard inputs/outputs. This is one of the most important things to understand to fully benefit from the Unix system.
|
||||
|
||||
## File Name Patterns with Wildcards
|
||||
|
||||
It's very common in a Unix command to need to specify multiple file names. When the number of files becomes large, typing these names one by one can be tedious, especially if all file names share common characteristics.
|
||||
|
||||
To address this, there's a series of "wildcard" characters to indicate the form of desired file names:
|
||||
|
||||
| Wildcard | Matches |
|
||||
|----------|---------|
|
||||
| `*` | Zero, one, or more characters |
|
||||
| `?` | Exactly one character |
|
||||
| `[...]` | One character from the list |
|
||||
| `[^...]` | One character NOT in the list |
|
||||
| `[a-z]` | One character in the range |
|
||||
|
||||
Each word in a Unix command line using these characters is replaced during execution by the list of existing file names matching the pattern.
|
||||
|
||||
```bash
|
||||
# List all text files
|
||||
$ ls *.txt
|
||||
|
||||
# Files starting with 'data' and any single character
|
||||
$ ls data?
|
||||
|
||||
# Files starting with uppercase letter
|
||||
$ ls [A-Z]*
|
||||
|
||||
# Files NOT starting with lowercase letter
|
||||
$ ls [^a-z]*
|
||||
|
||||
# Complex pattern
|
||||
$ ls experiment_[0-9][0-9].dat
|
||||
```
|
||||
|
||||
If no file matches the pattern, a "No match" error is generated.
|
||||
|
||||
```bash
|
||||
$ echo *toto
|
||||
bash: no matches found: *toto
|
||||
|
||||
$ ls /
|
||||
Applications Library bin home opt usr
|
||||
Desktop Network cores sbin private var
|
||||
Developer System dev etc tmp
|
||||
|
||||
$ echo /mach*
|
||||
/mach.sym /mach_kernel /mach_kernel.ctfsys
|
||||
|
||||
$ echo /*.*
|
||||
/atp.mol /mach.sym /mach_kernel.ctfsys /untitled.log
|
||||
|
||||
$ echo /[AD]*
|
||||
/Applications /Desktop_DB /Desktop_DF /Developer
|
||||
|
||||
$ echo /[uv]??
|
||||
/usr /var
|
||||
```
|
||||
|
||||
These file name patterns are most often used with file manipulation commands like copying (`cp`), deletion (`rm`), or listing (`ls`). They're also frequently used in loops to launch the same command on an entire series of datasets.
|
||||
|
||||
## Standard I/O Redirection
|
||||
|
||||
The property that gives a Unix shell its full power is the standard input/output redirection system. Each process inherits three standard data streams from its parent:
|
||||
|
||||
- `stdin`: Standard input stream (file descriptor 0)
|
||||
- `stdout`: Standard output stream (file descriptor 1)
|
||||
- `stderr`: Standard error stream (file descriptor 2)
|
||||
|
||||
```{mermaid}
|
||||
flowchart TB
|
||||
subgraph Default["Default Configuration"]
|
||||
Keyboard[("Keyboard")] --> stdin1["stdin"]
|
||||
stdin1 --> Shell1["Shell Process"]
|
||||
Shell1 --> stdout1["stdout"]
|
||||
Shell1 --> stderr1["stderr"]
|
||||
stdout1 --> Screen1[("Screen")]
|
||||
stderr1 --> Screen1
|
||||
end
|
||||
|
||||
style stdin1 fill:#e1f5ff
|
||||
style stdout1 fill:#e1ffe1
|
||||
style stderr1 fill:#ffe1e1
|
||||
```
|
||||
|
||||
### Redirecting Standard Output
|
||||
|
||||
To save results generated by a program to a file, add an output redirection instruction at the end of the command line: `>` followed by a file name.
|
||||
|
||||
```bash
|
||||
$ ls /
|
||||
Applications Desktop Developer Library System
|
||||
bin cores dev etc home usr var
|
||||
|
||||
$ ls / > my_listing
|
||||
|
||||
$ ls -l
|
||||
total 8
|
||||
drwxr-xr-x 2 alice staff 102 Nov 27 17:18 myprograms
|
||||
-rw-r--r-- 1 alice staff 241 Dec 3 16:50 my_listing
|
||||
|
||||
$ cat my_listing
|
||||
Applications
|
||||
Desktop
|
||||
Developer
|
||||
Library
|
||||
System
|
||||
bin
|
||||
cores
|
||||
dev
|
||||
etc
|
||||
home
|
||||
usr
|
||||
var
|
||||
```
|
||||
|
||||
```{mermaid}
|
||||
flowchart LR
|
||||
stdin["stdin"] --> Process["ls /"]
|
||||
Process --> stdout["stdout"]
|
||||
Process --> stderr["stderr"]
|
||||
stdout --> File[("my_listing")]
|
||||
stderr --> Screen[("Screen")]
|
||||
|
||||
style stdout fill:#e1ffe1
|
||||
style stderr fill:#ffe1e1
|
||||
```
|
||||
|
||||
Important notes:
|
||||
|
||||
- If the file doesn't exist, it's created and filled with results
|
||||
- If the file exists, it's erased and replaced with a new file
|
||||
- **Be careful**: This can easily overwrite existing files
|
||||
|
||||
To append results to an existing file instead of replacing it, use `>>`:
|
||||
|
||||
```bash
|
||||
$ echo "First line" > output.txt
|
||||
$ echo "Second line" >> output.txt
|
||||
$ cat output.txt
|
||||
First line
|
||||
Second line
|
||||
```
|
||||
|
||||
### Redirecting Standard Input
|
||||
|
||||
Input redirection indicates where a program reading from standard input should find its data. Input redirection uses the `<` character.
|
||||
|
||||
```bash
|
||||
$ grep or < my_listing
|
||||
Network
|
||||
cores
|
||||
|
||||
$ grep or < my_listing > my_selection
|
||||
|
||||
$ cat my_selection
|
||||
Network
|
||||
cores
|
||||
```
|
||||
|
||||
The `grep` command selects lines of text containing a pattern (or in this example) and copies them to standard output. Input redirection tells the process to read from `my_listing`, and output redirection saves results to `my_selection`.
|
||||
|
||||
### Redirecting Output to Another Process (Pipes)
|
||||
|
||||
The most powerful redirection mode connects one process's standard output to another's standard input. The first program's results become the second's data. Data passes directly between processes without going through an intermediate file. This creates a "pipe" between processes.
|
||||
|
||||
```{mermaid}
|
||||
flowchart LR
|
||||
stdin1["stdin"] --> P1["ls /"]
|
||||
P1 --> pipe["|<br/>pipe"]
|
||||
pipe --> P2["grep or"]
|
||||
P2 --> stdout2["stdout"]
|
||||
P2 --> stderr2["stderr"]
|
||||
stdout2 --> Screen[("Screen")]
|
||||
stderr2 --> Screen
|
||||
|
||||
style pipe fill:#fff2cc
|
||||
style stdout2 fill:#e1ffe1
|
||||
style stderr2 fill:#ffe1e1
|
||||
```
|
||||
|
||||
Syntactically, this is achieved by joining two or more commands with the `|` character:
|
||||
|
||||
```bash
|
||||
$ ls / | grep or
|
||||
Network
|
||||
cores
|
||||
|
||||
$ ls / | grep or > my_selection
|
||||
|
||||
$ cat my_selection
|
||||
Network
|
||||
cores
|
||||
```
|
||||
|
||||
In a complex command, a process is created for each command, and data simply transits from one to another.
|
||||
|
||||
**Important restrictions:**
|
||||
|
||||
- Commands before a pipe cannot redirect stdout to a file (already piped to next command)
|
||||
- Commands after a pipe cannot redirect stdin from a file (already receiving from previous command)
|
||||
|
||||
You can chain multiple pipes:
|
||||
|
||||
```bash
|
||||
# Count lines containing "error" in log file
|
||||
$ cat logfile.txt | grep error | wc -l
|
||||
|
||||
# Sort unique email addresses
|
||||
$ cat emails.txt | sort | uniq
|
||||
```
|
||||
|
||||
## Building Execution Loops
|
||||
|
||||
A computer's value lies in its ability to automatically perform repetitive calculation tasks. Users often find themselves needing to launch the same Unix command for calculations on multiple datasets. If each dataset is saved in a different file with coherent naming (e.g., `gis_vercors.dat`, `gis_belledonne.dat`, `gis_chartreuse.dat`), it's possible to leverage loop structures offered by Unix shells.
|
||||
|
||||
### Shell Variables
|
||||
|
||||
Working automatically and repetitively requires using variables to store useful, changing information at each iteration. For example, if your Unix command must read data from different files for each execution, you cannot write the file name in your command since it won't always be the same.
|
||||
|
||||
You already know environment variables, set up by the `export` command, used to store system configuration information. There are simple variables allowing you to store any information you deem necessary during your Unix session. They're set up with simple assignment:
|
||||
|
||||
```bash
|
||||
$ myvar="hello everyone"
|
||||
$ echo myvar
|
||||
myvar
|
||||
$ echo $myvar
|
||||
hello everyone
|
||||
```
|
||||
|
||||
To retrieve the value contained in a variable, precede its name with the `$` character.
|
||||
|
||||
### The `for` Loop
|
||||
|
||||
To solve our problem of repeating the same Unix command multiple times while working on different data files, we'll create a variable that takes each element of a list as its value in turn. In our case, this list will be a list of file names constructed using file name ambiguity characters.
|
||||
|
||||
```bash
|
||||
$ echo /[mnop]*
|
||||
/mach.sym /mach_kernel /mach_kernel.ctfsys /net /opt /private
|
||||
|
||||
$ for f in /[mnop]*; do
|
||||
> echo "Working with file $f"
|
||||
> done
|
||||
Working with file /mach.sym
|
||||
Working with file /mach_kernel
|
||||
Working with file /mach_kernel.ctfsys
|
||||
Working with file /net
|
||||
Working with file /opt
|
||||
Working with file /private
|
||||
```
|
||||
|
||||
```{mermaid}
|
||||
flowchart TD
|
||||
Start([Start]) --> Init["Initialize loop variable<br/>with first item"]
|
||||
Init --> Check{More items<br/>in list?}
|
||||
Check -->|Yes| Execute["Execute commands<br/>in loop body"]
|
||||
Execute --> Next["Move to next item"]
|
||||
Next --> Check
|
||||
Check -->|No| End([End])
|
||||
|
||||
style Execute fill:#e1ffe1
|
||||
```
|
||||
|
||||
The syntax is:
|
||||
|
||||
```bash
|
||||
for variable in list; do
|
||||
commands using $variable
|
||||
done
|
||||
```
|
||||
|
||||
All Unix commands inserted between `do` and `done` are executed once for each value taken by the variable.
|
||||
|
||||
Practical examples:
|
||||
|
||||
```bash
|
||||
# Process multiple data files
|
||||
$ for file in data*.txt; do
|
||||
> echo "Processing $file"
|
||||
> ./analyze.sh $file > results_$file
|
||||
> done
|
||||
|
||||
# Rename multiple files
|
||||
$ for file in *.jpeg; do
|
||||
> mv "$file" "${file%.jpeg}.jpg"
|
||||
> done
|
||||
|
||||
# Create numbered directories
|
||||
$ for i in {1..10}; do
|
||||
> mkdir experiment_$i
|
||||
> done
|
||||
```
|
||||
|
||||
### Conditional Execution
|
||||
|
||||
Bash also provides conditional structures:
|
||||
|
||||
```bash
|
||||
# if-then-else
|
||||
$ if [ -f "data.txt" ]; then
|
||||
> echo "File exists"
|
||||
> else
|
||||
> echo "File not found"
|
||||
> fi
|
||||
|
||||
# Test file properties
|
||||
$ for file in *.txt; do
|
||||
> if [ -s "$file" ]; then
|
||||
> echo "$file is not empty"
|
||||
> fi
|
||||
> done
|
||||
```
|
||||
|
||||
Common test operators:
|
||||
|
||||
| Test | Meaning |
|
||||
|------|---------|
|
||||
| `-f file` | File exists and is regular file |
|
||||
| `-d dir` | Directory exists |
|
||||
| `-s file` | File exists and is not empty |
|
||||
| `-r file` | File is readable |
|
||||
| `-w file` | File is writable |
|
||||
| `-x file` | File is executable |
|
||||
|
||||
# Essential Unix Commands (Alphabetical)
|
||||
|
||||
The commands presented here are a subset of all commands available by default on a Unix system. They're presented with a subset of their options. For a complete description of their functionality, refer to online help accessible via the `man` command.
|
||||
|
||||
## `awk` - Pattern Scanning and Processing
|
||||
|
||||
Named after its authors (Aho, Weinberger, Kernighan), `awk` is a complete programming language. A full description is beyond this course's scope but was perfectly described in "The AWK Programming Language" by its authors.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
awk [-F separator] 'program' [data_file]
|
||||
```
|
||||
|
||||
**Main options:**
|
||||
|
||||
- `-F` - Specify column separator
|
||||
|
||||
**Examples:**
|
||||
```bash
|
||||
# Print second column
|
||||
$ awk '{print $2}' file.txt
|
||||
|
||||
# Sum numbers in first column
|
||||
$ awk '{sum += $1} END {print sum}' numbers.txt
|
||||
|
||||
# Process CSV file
|
||||
$ awk -F',' '{print $1, $3}' data.csv
|
||||
```
|
||||
|
||||
## `bash` - Bourne-Again Shell
|
||||
|
||||
Launches a bash Unix shell. To exit this new shell, press `Ctrl-D` at a prompt.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
bash
|
||||
```
|
||||
|
||||
**Example:**
|
||||
```bash
|
||||
$ bash
|
||||
bash-5.1$ export test_var="hello"
|
||||
bash-5.1$ exit
|
||||
$
|
||||
```
|
||||
|
||||
## `bg` - Send Process to Background
|
||||
|
||||
Resumes execution of a process suspended by `Ctrl-Z` in the background.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
bg [%job]
|
||||
```
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- `%job` - Job number (preceded by %). Get list with `jobs` command.
|
||||
|
||||
**Example:**
|
||||
```bash
|
||||
$ sleep 30
|
||||
^Z
|
||||
[1]+ Stopped sleep 30
|
||||
$ jobs
|
||||
[1]+ Stopped sleep 30
|
||||
$ bg %1
|
||||
[1]+ sleep 30 &
|
||||
$ jobs
|
||||
[1]+ Running sleep 30 &
|
||||
```
|
||||
|
||||
## `cat` - Concatenate Files
|
||||
|
||||
Reads content from one or more data streams and copies it identically to standard output.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
cat [file ...]
|
||||
```
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- `file` - One or more file names. If none provided, reads from stdin.
|
||||
|
||||
**Examples:**
|
||||
```bash
|
||||
# Display file content
|
||||
$ cat file.txt
|
||||
|
||||
# Concatenate multiple files
|
||||
$ cat file1.txt file2.txt > combined.txt
|
||||
|
||||
# Number lines
|
||||
$ cat -n file.txt
|
||||
```
|
||||
|
||||
## `cd` - Change Directory
|
||||
|
||||
Changes the current working directory.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
cd [directory]
|
||||
```
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- `directory` - New working directory name. Without argument, returns to home.
|
||||
|
||||
**Examples:**
|
||||
```bash
|
||||
$ pwd
|
||||
/home/alice
|
||||
$ cd /usr/local
|
||||
$ pwd
|
||||
/usr/local
|
||||
$ cd ../../home/alice
|
||||
$ pwd
|
||||
/home/alice
|
||||
$ cd
|
||||
$ pwd
|
||||
/home/alice
|
||||
```
|
||||
|
||||
## `chmod` - Change File Mode
|
||||
|
||||
Changes file access permissions.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
chmod [-R] mode file
|
||||
```
|
||||
|
||||
**Main options:**
|
||||
|
||||
- `-R` - Recursive operation on directory contents
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- `mode` - Permission change description (e.g., `u+x`, `go-w`, `755`)
|
||||
- `file` - File(s) whose mode should be changed
|
||||
|
||||
**Examples:**
|
||||
```bash
|
||||
# Add execute permission for user
|
||||
$ chmod u+x script.sh
|
||||
|
||||
# Remove write permission for group and others
|
||||
$ chmod go-w data.txt
|
||||
|
||||
# Set specific permissions with octal
|
||||
$ chmod 755 program
|
||||
|
||||
# Recursive permission change
|
||||
$ chmod -R 644 documents/
|
||||
```
|
||||
|
||||
## `cp` - Copy Files
|
||||
|
||||
Copies a file or directory.
|
||||
|
||||
**Synopsis:**
|
||||
```bash
|
||||
cp [-R] source destination
|
||||
```
|
||||
|
||||
**Main options:**
|
||||
|
||||
- `-R` - Recursive copy for directories
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- `source` - File(s) to be copied
|
||||
- `destination` - Copy destination name or directory
|
||||
|
||||
**Examples:**
|
||||
```bash
|
||||
# Copy file
|
||||
$ cp source.txt backup.txt
|
||||
|
||||
# Copy to directory
|
||||
$ cp file.txt documents/
|
||||
|
||||
# Copy directory recursively
|
||||
$ cp -R project/ project_backup/
|
||||
|
||||
# Copy multiple files to directory
|
||||
$
|
||||
1248
web_src/05_Lectures/05_Metabarcoding/Biodiversity_indices/Slides.qmd
Normal file
1248
web_src/05_Lectures/05_Metabarcoding/Biodiversity_indices/Slides.qmd
Normal file
File diff suppressed because it is too large
Load Diff
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|
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|
||||
%% This BibTeX bibliography file was created using BibDesk.
|
||||
%% http://bibdesk.sourceforge.net/
|
||||
|
||||
|
||||
%% Created for Eric Coissac at 2018-10-18 14:52:51 +0200
|
||||
|
||||
|
||||
%% Saved with string encoding Unicode (UTF-8)
|
||||
|
||||
|
||||
|
||||
@article{Tsallis:94:00,
|
||||
Author = {Tsallis, Constantino},
|
||||
Date-Added = {2018-10-18 14:52:41 +0200},
|
||||
Date-Modified = {2018-10-18 14:52:49 +0200},
|
||||
Journal = {Quim. Nova},
|
||||
Number = 6,
|
||||
Pages = {468--471},
|
||||
Title = {What are the numbers that experiments provide},
|
||||
Volume = 17,
|
||||
Year = 1994}
|
||||
|
||||
|
||||
@ARTICLE{Whittaker:10:00,
|
||||
title = "Meta-analyses and mega-mistakes: calling time on meta-analysis
|
||||
of the species richness-productivity relationship",
|
||||
author = "Whittaker, Robert J",
|
||||
abstract = "The form of the species richness-productivity relationship
|
||||
(SRPR) is both theoretically important and contentious. In an
|
||||
effort to distill general patterns, ecologists have undertaken
|
||||
meta-analyses, within which each SRPR data set is first
|
||||
classified into one of five alternative forms: positive, humped
|
||||
(unimodal), negative, U-shaped (unimodal), and no relationship.
|
||||
Herein, I first provide a critique of this approach, based on 68
|
||||
plant data sets/ studies used in three meta-analyses published
|
||||
in Ecology. The meta-analyses are shown to have resulted in
|
||||
highly divergent outcomes, inconsistent and often highly
|
||||
inappropriate classification of data sets, and the introduction
|
||||
and multiplication of errors from one meta-analysis to the next.
|
||||
I therefore call on the ecological community at large to adopt a
|
||||
far more rigorous and critical attitude to the use of
|
||||
meta-analysis. Second, I develop the argument that the
|
||||
literature on the SRPR continues to be bedeviled by a common
|
||||
failing to appreciate the fundamental importance of the scale of
|
||||
analysis, beginning with the confusion evident between concepts
|
||||
of grain, focus, and extent. I postulate that variation in the
|
||||
form of the SRPR at fine scales of analysis owes much to
|
||||
artifacts of the sampling regime adopted. An improved
|
||||
understanding may emerge from combining sampling theory with an
|
||||
understanding of the factors controlling the form of species
|
||||
abundance distributions and species accumulation curves.",
|
||||
journal = "Ecology",
|
||||
publisher = "Eco Soc America",
|
||||
volume = 91,
|
||||
number = 9,
|
||||
pages = "2522--2533",
|
||||
month = sep,
|
||||
year = 2010
|
||||
}
|
||||
|
||||
11
web_src/05_Lectures/slides.css
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11
web_src/05_Lectures/slides.css
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|
||||
/* Centre toutes les images dans les slides */
|
||||
|
||||
.reveal {
|
||||
font-size: 1.5em;
|
||||
}
|
||||
|
||||
.quarto-figure-default {
|
||||
display: block;
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
}
|
||||
Reference in New Issue
Block a user