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29 lines
1.5 KiB
Markdown
29 lines
1.5 KiB
Markdown
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# Semantic Description of `obiseq` Expression-Based Workers
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This module provides **expression-driven transformation workers** for biological sequence objects (`BioSequence`). It leverages a custom expression language (via `OBILang`) to dynamically compute values based on sequence metadata and content.
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## Core Components
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- **`Expression(expression string)`**:
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Returns a function that evaluates the given expression in context. The evaluation scope includes:
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- `annotations`: sequence annotations (metadata).
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- `sequence`: the full `BioSequence` object itself.
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- **`EditIdWorker(expression string)`**:
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A sequence worker that updates the *ID* of a `BioSequence` by evaluating the expression.
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- On success: sets `sequence.Id()` to string representation of result.
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- On failure: logs and returns an error with context.
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- **`EditAttributeWorker(key string, expression string)`**:
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A sequence worker that sets a *custom attribute* (identified by `key`) on the sequence, using evaluated expression result.
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- Supports arbitrary metadata enrichment.
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- Errors are reported with sequence ID and failed expression.
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## Use Cases
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- Generate new IDs from annotation fields (e.g., `"gene_" + annotations["locus_tag"]`).
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- Compute and store derived attributes (e.g., GC content, ORF length) as sequence metadata.
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- Apply conditional logic or transformations across large sets of sequences in pipelines.
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All workers conform to the `SeqWorker` interface, enabling composition and chaining.
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