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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)
32 lines
1.7 KiB
Markdown
32 lines
1.7 KiB
Markdown
## NCBI Taxonomy Archive Support in `obiformats`
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This Go package provides utilities for handling **NCBI Taxonomy dumps archived as `.tar` files**.
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### Core Functionalities
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1. **Archive Validation (`IsNCBITarTaxDump`)**
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- Checks whether a given `.tar` file contains all required NCBI Taxonomy dump files: `citations.dmp`, `division.dmp`, `gencode.dmp`, `names.dmp`, `delnodes.dmp`, `gc.prt`, `merged.dmp`, and `nodes.dmp`.
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- Returns a boolean indicating if the archive is a complete NCBI tax dump.
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2. **Taxonomy Loading (`LoadNCBITarTaxDump`)**
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- Parses the `.tar` archive and extracts key files to build a `Taxonomy` object.
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- Steps include:
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- **Nodes**: Loads taxonomic hierarchy (`nodes.dmp`) via `loadNodeTable`.
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- **Names**: Parses scientific and common names (`names.dmp`) via `loadNameTable`, with an option to load *only scientific names* (`onlysn`).
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- **Merged Taxa**: Integrates taxonomic aliases from `merged.dmp`, using `loadMergedTable`.
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- Sets the root taxon to NCBI’s default (`taxid = 1`, i.e., *root*).
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3. **Integration with Other Modules**
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- Uses `obiutils.Ropen`, `TarFileReader` for robust file handling.
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- Leverages `obitax.Taxonomy`, a structured representation of taxonomic data.
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### Key Parameters
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- `onlysn`: If true, only scientific names are loaded (reduces memory usage).
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- `seqAsTaxa`: Reserved for future use; currently unused.
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### Logging & Error Handling
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- Uses `logrus` to log loading progress and counts.
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- Returns descriptive errors if required files or the root taxon are missing.
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> **Note**: Designed for efficient, standards-compliant ingestion of NCBI Taxonomy data in bioinformatics pipelines.
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