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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
28 lines
1.2 KiB
Markdown
28 lines
1.2 KiB
Markdown
# Semantic Description of `obiseq` Package
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The `obiseq` package provides utilities for handling **IUPAC nucleotide ambiguity codes** in biological sequences.
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## Core Components
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- `_iupac`: A lookup table mapping lowercase ASCII letters (`a`–`z`) to numeric IUPAC nucleotide codes:
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- `A=1`, `C=2`, `G=4`, `T/U=8` (standard bases)
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- Ambiguous codes are bitwise OR combinations:
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e.g., `R = A|G = 1+4=5`, `Y = C|T = 2+8=10`, etc.
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- Invalid or non-nucleotide characters map to `0`.
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## Key Functionality
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### `SameIUPACNuc(a, b byte) bool`
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Performs **case-insensitive comparison** of two nucleotide symbols using IUPAC ambiguity rules.
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- Converts uppercase letters to lowercase via bitwise OR (`|= 32`).
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- For valid nucleotides, checks if their IUPAC codes have **non-zero bitwise AND**:
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- Returns `true` only if the symbols share at least one possible base.
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*Example*: `'R' & 'A' → (5 & 1) = 1 > 0 ⇒ true`
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`'Y' & 'G' → (10 & 4) = 0 ⇒ false`
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- For non-IUPAC or invalid characters, falls back to exact equality (`a == b`).
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## Use Case
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Enables robust comparison of DNA/RNA sequences where ambiguity codes (e.g., `N`, `R`, `W`) are used—critical for alignment, variant calling, or primer design tools.
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