mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
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)
25 lines
1.6 KiB
Markdown
25 lines
1.6 KiB
Markdown
# `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.
|