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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

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`CSVTaxaIterator` Function — Semantic Description

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.

Core Functionality:

Input: A pointer-based taxonomic iterator (*obitax.ITaxon) and optional configuration via WithOption.
Output: An asynchronous CSV record iterator (*obiitercsv.ICSVRecord) that yields batches of records.

Configurable Output Fields (via options):

query: Taxon-associated query identifier, if enabled (WithPattern).
taxid: Either raw node ID (e.g., string pointer) or formatted taxon path (WithRawTaxid toggle).
parent: Parent taxonomic ID or string representation, if enabled (WithParent).
taxonomic_rank: Taxon rank (e.g., "species", "genus").
scientific_name: Full scientific name of the taxon.
Custom metadata fields: Specified via WithMetadata, extracted from taxon metadata store.
path: Full lineage path (e.g., "k__Bacteria; p__; c__..."), if enabled (WithPath).

Implementation Highlights:

Uses goroutines for non-blocking push of batches and clean shutdown (WaitAndClose, Done).
Supports batching (configurable via BatchSize) to optimize I/O.
Dynamically builds CSV headers based on selected options before processing begins.

Use Case:

Efficient, memory-light conversion of large taxonomic datasets (e.g., from classification pipelines) into structured CSV for downstream analysis or reporting.

1.6 KiB Raw Blame History

CSVTaxaIterator Function — Semantic Description