obitools4/autodoc/docmd/pkg/obiformats/taxonomy_read.md

Taxonomy Loading Module (obiformats)

This Go package provides semantic functionality to automatically detect and load taxonomic data from various file formats. It supports flexible, format-agnostic taxonomy ingestion via a unified interface.

Core Features

1. Format Detection

   • DetectTaxonomyFormat(path) identifies the taxonomy source format by inspecting file type (directory, MIME-type), filename patterns, or structure.
   • Supports:
     • NCBI Taxdump (both directory and .tar archive)
     • CSV files (text/csv)
     • FASTA/FASTQ sequences (via mimetype detection)

2. Modular Loaders

   • Returns a typed TaxonomyLoader function, enabling deferred loading with configurable options (onlysn, seqAsTaxa).
   • Each loader abstracts format-specific parsing (e.g., NCBI nodes.dmp, FASTA header taxonomy extraction).

3. Sequence-Based Taxonomy Extraction

   • For sequence files (FASTA/FASTQ), taxonomy is inferred from headers or associated metadata, using ExtractTaxonomy().

4. Integration with OBITools Ecosystem

   • Leverages obitax.Taxonomy as the canonical output structure.
   • Uses custom MIME-type registration (obiutils.RegisterOBIMimeType()) for robust detection of bioinformatics formats.

5. Error Handling & Logging

   • Graceful failure with descriptive errors; informative logging via logrus.

Usage Flow

tax, err := LoadTaxonomy("path/to/data", onlysn=true, seqAsTaxa=false)

The module enables interoperability across taxonomic data sources in metabarcoding workflows.