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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)
27 lines
1.5 KiB
Markdown
27 lines
1.5 KiB
Markdown
# Taxonomic Classification via `TaxonomyClassifier`
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The `obiseq` package provides a taxonomic classification mechanism through the `TaxonomyClassifier` function.
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- **Purpose**: Constructs a reusable classifier for biological sequences based on taxonomic hierarchy.
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- **Inputs**:
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- `taxonomicRank`: Target rank (e.g., `"species"`, `"genus"`).
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- `taxonomy`: Reference taxonomy (`*obitax.Taxonomy`), with fallback via `.OrDefault(true)`.
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- `abortOnMissing`: Boolean flag to enforce strict taxon resolution.
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- **Core Logic**:
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- For each sequence, retrieves its `Taxon`, then drills down to the requested rank using `.TaxonAtRank()`.
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- If `abortOnMissing` is true, exits on failure to resolve the taxon or rank.
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- Internally maps `*TaxNode`s to integer codes for efficient storage/comparison.
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- **Returned Object (`BioSequenceClassifier`)**:
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- `Code(sequence) int`: Assigns a unique integer code to the taxonomic assignment of a sequence.
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- `Value(code) string`: Returns the scientific name corresponding to a code.
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- `Reset()`: Reinitializes internal mappings (useful for batch processing).
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- `Clone() *BioSequenceClassifier`: Creates a fresh, identical classifier instance.
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- **Design Rationale**:
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- Uses integer codes to avoid repeated string operations and enable fast indexing (e.g., for counting).
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- Supports both strict (`abortOnMissing=true`) and lenient classification modes.
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This design enables scalable, efficient taxonomic profiling of sequencing datasets.
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