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42 lines
2.3 KiB
Markdown
42 lines
2.3 KiB
Markdown
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# Taxonomic Annotation Features in `obiseq` Package
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This package provides semantic taxonomic annotation capabilities for biological sequences (`BioSequence`). It integrates with a taxonomy database to assign, retrieve, and manage taxonomic identifiers (taxids) and related metadata.
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## Core Functions
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- **`Taxid()`**: Retrieves the taxonomic ID as a string (e.g., `"12345"` or `"NA"`), supporting multiple internal representations (`string`, `int`, `float64`). Returns `"NA"` if no taxid is set.
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- **`Taxon(taxonomy)`**: Returns the corresponding `*obitax.Taxon` object, or `nil` if taxid is `"NA"`.
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- **`SetTaxid(taxid, rank...)`**: Assigns a taxonomic ID to the sequence. Validates against default taxonomy; handles aliases and errors based on configuration flags (`FailOnTaxonomy`, `UpdateTaxid`). Optionally stores taxid under a custom rank (e.g., `"genus_taxid"`).
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- **`SetTaxon(taxon, rank...)`**: Assigns a `*obitax.Taxon` object directly; stores its string representation as taxid.
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## Rank-Specific Annotation
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- **`SetTaxonAtRank(taxonomy, rank)`**: Annotates the sequence with taxid and scientific name at a specified Linnaean rank (e.g., `"species"`, `"genus"`). Sets two attributes: `rank_taxid` and `rank_name`. Returns the taxon at that rank (or `nil`).
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- **Convenience wrappers**:
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- `SetSpecies(...)`
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- `SetGenus(...)`
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- `SetFamily(...)`
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All delegate to `SetTaxonAtRank`.
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## Taxonomic Path & Metadata
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- **`SetPath(taxonomy)`**: Computes and stores the full taxonomic lineage (from root to species) as a string slice under attribute `"taxonomic_path"`.
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- **`Path()`**: Retrieves the stored taxonomic path; recomputes it if missing and a default taxonomy exists.
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- **`SetScientificName(taxonomy)`**: Stores the sequence’s species-level scientific name under `"scientific_name"`.
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- **`SetTaxonomicRank(taxonomy)`**: Stores the taxon’s rank (e.g., `"species"`, `"genus"`) under `"taxonomic_rank"`.
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## Error Handling & Configuration
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- Uses `logrus` and custom logging (`obilog`) for warnings/errors.
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- Behavior on taxonomy mismatches (e.g., unknown taxid, alias) is configurable via `obidefault` settings.
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- Ensures type consistency: taxid must be string, int, or float; invalid types trigger fatal errors.
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All methods are designed for seamless integration into bioinformatics pipelines, enabling robust taxonomic profiling of sequencing data.
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