get-tax-info 0.2.0

Convert NCBI TaxIDs to scientific species names and vice-versa

get-tax-info

Load NCBI taxonomy (names.dmp and nodes.dmp) into a SQLite database for lightning-fast hash-based lookups.

Features

• Fast: Indexed SQLite queries for names, parents, and children.
• Automatic: Downloads and converts NCBI data on first run.
• Easy Storage: Uses standard user cache directories by default.
• BUSCO Integration: Maps TaxIDs to the best BUSCO dataset for lineage analysis.

Installation

pip install git+https://github.com/MrTomRod/get-tax-info

Configuration

By default, the database is stored in the user cache directory (e.g., ~/.cache/get-tax-info/).

• Change location: Set GET_TAX_INFO_DB environment variable or pass db_path to GetTaxInfo.

Python Usage

from get_tax_info import GetTaxInfo, TaxID

# Automatically download/init data on first use
gti = GetTaxInfo()

# Use the TaxID object (recommended)
t = gti.get_taxid_object(2590146)  # Ektaphelenchus kanzakii
print(t.scientific_name, t.rank)   # 'Ektaphelenchus kanzakii', 'species'

# Parents and children
parent = t.parent                  # <TaxID 483517 (Ektaphelenchus)>
children = parent.children          # List of TaxID objects

# Ancestor at specific rank
genus = t.tax_at_rank('genus')

CLI Usage

# Get BUSCO dataset for a TaxID
get-tax-info taxid-to-busco-dataset --taxid 110

# Add TaxID and BUSCO column to a CSV/TSV table
get-tax-info add-taxid-column table.tsv --sep ,

A complete demonstration of the BUSCO workflow (including Podman usage) can be found in demo_busco_workflow.sh.

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Note: BUSCO dataset mapping requires pre-downloaded lineages. See get_busco.py for details.