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)
1.7 KiB
MakeSetAttributeWorker Functionality Overview
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
rankis part of a predefined taxonomic hierarchy (taxonomy.RankList()). If invalid, it terminates execution with an informative error. -
Worker construction: It returns a closure (
obiiter.SeqWorker) — essentially a function that transforms biological sequences. -
Core behavior: For each input
*obiseq.BioSequence, it callstaxonomy.SetTaxonAtRank(sequence, rank). This likely assigns or updates the taxonomic label (e.g., species, genus) at the specified rank in the sequence’s metadata. -
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
BioSequencein-place (via mutation of its taxonomic metadata), then returns it. -
Use case example:
worker := MakeSetAttributeWorker("species") seq = worker(seq) // annotates `seq` with species-level taxon -
Assumptions:
taxonomy.SetTaxonAtRankexists and handles rank-specific taxon assignment.- Taxonomic ranks are ordered, finite, and validated (e.g.,
["domain", "phylum", ..., "species"]). - Sequences carry mutable taxonomic metadata.
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Error handling: Fails fast on invalid rank input, preventing silent misannotation.