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

NCBI Taxonomy Archive Support in obiformats

This Go package provides utilities for handling NCBI Taxonomy dumps archived as .tar files.

Core Functionalities

1. Archive Validation (IsNCBITarTaxDump)

   • 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.
   • Returns a boolean indicating if the archive is a complete NCBI tax dump.

2. Taxonomy Loading (LoadNCBITarTaxDump)

   • Parses the .tar archive and extracts key files to build a Taxonomy object.
   • Steps include:
     • Nodes: Loads taxonomic hierarchy (nodes.dmp) via loadNodeTable.
     • Names: Parses scientific and common names (names.dmp) via loadNameTable, with an option to load only scientific names (onlysn).
     • Merged Taxa: Integrates taxonomic aliases from merged.dmp, using loadMergedTable.
   • Sets the root taxon to NCBI’s default (taxid = 1, i.e., root).

3. Integration with Other Modules

   • Uses obiutils.Ropen, TarFileReader for robust file handling.
   • Leverages obitax.Taxonomy, a structured representation of taxonomic data.

Key Parameters

• onlysn: If true, only scientific names are loaded (reduces memory usage).
• seqAsTaxa: Reserved for future use; currently unused.

Logging & Error Handling

• Uses logrus to log loading progress and counts.
• Returns descriptive errors if required files or the root taxon are missing.

Note

: Designed for efficient, standards-compliant ingestion of NCBI Taxonomy data in bioinformatics pipelines.