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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)
25 lines
1.6 KiB
Markdown
25 lines
1.6 KiB
Markdown
# `ExtractTaxonomy` Function — Semantic Description
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The `ExtractTaxonomy` method is a core utility in the `obiiter` package, designed to aggregate taxonomic information across biological sequences processed by an iterator.
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- **Input**:
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- A pointer to `IBioSequence`, representing a sequence iterator over biological data.
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- A boolean flag `seqAsTaxa`: if true, each full sequence is treated as a single taxonomic unit; otherwise, individual elements within slices are processed separately.
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- **Process**:
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- Iterates through all sequences via `iterator.Next()` and retrieves each current slice using `Get().Slice()`.
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- For every slice, it calls the underlying `.ExtractTaxonomy()` method (from `obitax`), progressively building or updating a shared `*obitax.Taxonomy` object.
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- Stops and returns immediately upon encountering the first error during taxonomy extraction.
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- **Output**:
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- Returns a fully populated `*obitax.Taxonomy` object (or partial result if early failure occurs).
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- Returns `nil` error on success; otherwise, returns the first encountered error.
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- **Semantic Role**:
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Enables scalable taxonomic profiling of high-throughput sequencing data by delegating per-slice extraction logic to the `obitax` module, while ensuring robust iteration and error handling.
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- **Dependencies**:
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Relies on `obitax.Taxonomy` for structured taxonomic representation and assumes slices implement the `.ExtractTaxonomy()` interface.
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This function exemplifies a *map-reduce*-style pattern: mapping taxonomy extraction over slices, and reducing results into a unified taxonomic summary.
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