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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)
35 lines
1.6 KiB
Markdown
35 lines
1.6 KiB
Markdown
# Taxonomy Loading Module (`obiformats`)
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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.
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## Core Features
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1. **Format Detection**
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- `DetectTaxonomyFormat(path)` identifies the taxonomy source format by inspecting file type (directory, MIME-type), filename patterns, or structure.
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- Supports:
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• NCBI Taxdump (both directory and `.tar` archive)
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• CSV files (`text/csv`)
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• FASTA/FASTQ sequences (via `mimetype` detection)
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2. **Modular Loaders**
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- Returns a typed `TaxonomyLoader` function, enabling deferred loading with configurable options (`onlysn`, `seqAsTaxa`).
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- Each loader abstracts format-specific parsing (e.g., NCBI `nodes.dmp`, FASTA header taxonomy extraction).
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3. **Sequence-Based Taxonomy Extraction**
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- For sequence files (FASTA/FASTQ), taxonomy is inferred from headers or associated metadata, using `ExtractTaxonomy()`.
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4. **Integration with OBITools Ecosystem**
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- Leverages `obitax.Taxonomy` as the canonical output structure.
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- Uses custom MIME-type registration (`obiutils.RegisterOBIMimeType()`) for robust detection of bioinformatics formats.
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5. **Error Handling & Logging**
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- Graceful failure with descriptive errors; informative logging via `logrus`.
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## Usage Flow
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```go
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tax, err := LoadTaxonomy("path/to/data", onlysn=true, seqAsTaxa=false)
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```
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The module enables interoperability across taxonomic data sources in metabarcoding workflows.
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