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18 lines
1.3 KiB
Markdown
18 lines
1.3 KiB
Markdown
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# NCBI Taxonomy Loader Module (`obiformats`)
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This Go package provides functionality to parse and load NCBI taxonomy dump files into a structured `Taxonomy` object. It supports three core file types:
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- **nodes.dmp**: Defines the taxonomic hierarchy via `taxid|parent_taxid|rank` records.
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- **names.dmp**: Maps taxonomic IDs to names and name classes (e.g., "scientific name", "common name").
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- **merged.dmp**: Tracks deprecated taxonomic IDs and their replacements.
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Key features:
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- Custom CSV parsing with `|` delimiter, comment support (`#`), and whitespace trimming.
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- Support for loading *only scientific names* via the `onlysn` flag in `LoadNCBITaxDump`.
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- Efficient buffered reading (`bufio.Reader`) for large files.
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- Automatic root taxon (taxid `"1"`, i.e., *root*) assignment after loading.
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- Alias resolution: deprecated taxids are mapped to current ones via `AddAlias`.
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- Robust error handling with fatal logging on critical failures (e.g., missing root taxon, invalid parent references).
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The main entry point is `LoadNCBITaxDump(directory string, onlysn bool)`, which constructs a fully initialized taxonomy from NCBI dump files. Designed for integration with `obitax` and `obiutils`, it enables downstream applications (e.g., metabarcoding pipelines) to perform taxonomic queries and filtering.
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