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mlstdb

Tests PyPI Bioconda

Keep your mlst databases up to date with.. just two commands

mlstdb handles the OAuth authentication required to access PubMLST and BIGSdb Pasteur APIs, downloads the latest MLST schemes, and builds a ready-to-use BLAST database for the mlst tool.

Why mlstdb?

The mlst tool comes with a bundled database, but MLST schemes are continuously updated on PubMLST and Pasteur. Keeping your local database current requires authentication setup (OAuth2) and downloading files. mlstdb handles all of that with additional features.

What it does:

  • Handles OAuth registration and token management for PubMLST and Pasteur
  • Downloads allele sequences and ST profiles for curated MLST schemes
  • Builds the BLAST database that mlst needs
  • Supports parallel downloads, resume on failure, and custom scheme lists

Quick Start

# 1. Install
conda create -n mlst -c bioconda mlst && conda activate mlst
pip install mlstdb

# 2. Connect to databases (one-time setup)
mlstdb connect --db pubmlst
mlstdb connect --db pasteur

# 3. Download schemes and build BLAST database
mlstdb update

# 4. Use with mlst
mlst --blastdb blast/mlst.fa --datadir pubmlst your_assembly.fasta

See the Getting Started guide for a detailed walkthrough.

Commands at a Glance

Command Purpose
mlstdb connect Register OAuth credentials with PubMLST or Pasteur
mlstdb update Download schemes and build the BLAST database
mlstdb fetch (Advanced) Explore and filter all available schemes

Most users only need connect and update. See the Usage Overview for details.

Next Steps