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25 lines
1.6 KiB
Markdown
25 lines
1.6 KiB
Markdown
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# `CSVTaxaIterator` Function — Semantic Description
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The function `CSVTaxaIterator`, part of the `obiformats` package, converts a taxonomic iterator (`*obitax.ITaxon`) into an **incremental CSV record generator** via `obiitercsv.ICSVRecord`. It enables streaming, batched export of taxonomic data to CSV format with configurable fields.
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### Core Functionality:
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- **Input**: A pointer-based taxonomic iterator (`*obitax.ITaxon`) and optional configuration via `WithOption`.
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- **Output**: An asynchronous CSV record iterator (`*obiitercsv.ICSVRecord`) that yields batches of records.
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### Configurable Output Fields (via options):
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- `query`: Taxon-associated query identifier, if enabled (`WithPattern`).
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- `taxid`: Either raw node ID (e.g., string pointer) or formatted taxon path (`WithRawTaxid` toggle).
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- `parent`: Parent taxonomic ID or string representation, if enabled (`WithParent`).
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- `taxonomic_rank`: Taxon rank (e.g., "species", "genus").
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- `scientific_name`: Full scientific name of the taxon.
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- Custom metadata fields: Specified via `WithMetadata`, extracted from taxon metadata store.
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- `path`: Full lineage path (e.g., "k__Bacteria; p__; c__..."), if enabled (`WithPath`).
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### Implementation Highlights:
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- Uses **goroutines** for non-blocking push of batches and clean shutdown (`WaitAndClose`, `Done`).
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- Supports **batching** (configurable via `BatchSize`) to optimize I/O.
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- Dynamically builds CSV headers based on selected options before processing begins.
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### Use Case:
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Efficient, memory-light conversion of large taxonomic datasets (e.g., from classification pipelines) into structured CSV for downstream analysis or reporting.
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