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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)
29 lines
1.7 KiB
Markdown
29 lines
1.7 KiB
Markdown
# `MakeSetAttributeWorker` Functionality Overview
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The function `MakeSetAttributeWorker(rank string) obiiter.SeqWorker` constructs a reusable sequence-processing worker for taxonomic annotation.
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- **Input validation**: It first verifies that the provided `rank` is part of a predefined taxonomic hierarchy (`taxonomy.RankList()`). If invalid, it terminates execution with an informative error.
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- **Worker construction**: It returns a closure (`obiiter.SeqWorker`) — essentially a function that transforms biological sequences.
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- **Core behavior**: For each input `*obiseq.BioSequence`, it calls `taxonomy.SetTaxonAtRank(sequence, rank)`. This likely assigns or updates the taxonomic label (e.g., species, genus) at the specified rank in the sequence’s metadata.
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- **Purpose**: Enables modular, pipeline-friendly taxonomic annotation — e.g., in bioinformatics workflows where sequences must be annotated hierarchically (e.g., from phylum down to species).
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- **Design pattern**: Follows the *functional factory* and *worker interface* patterns, promoting composability in sequence processing pipelines.
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- **Side effects**: Modifies the input `BioSequence` *in-place* (via mutation of its taxonomic metadata), then returns it.
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- **Use case example**:
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```go
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worker := MakeSetAttributeWorker("species")
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seq = worker(seq) // annotates `seq` with species-level taxon
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```
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- **Assumptions**:
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- `taxonomy.SetTaxonAtRank` exists and handles rank-specific taxon assignment.
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- Taxonomic ranks are ordered, finite, and validated (e.g., `["domain", "phylum", ..., "species"]`).
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- Sequences carry mutable taxonomic metadata.
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- **Error handling**: Fails fast on invalid rank input, preventing silent misannotation.
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