kincekara / pubmlst

Query contigs on PubMLST via RESTful API

pubmlst

A simple python wrapper for querying sequences on PubMLST via RESTful API.

Requirements

Python3 on the path and requests module are required to run pubmlst script.

sudo apt-get install python3-requests
or
pip install requests

Example usage

# list available MLST organisms
pubmlst list

# ST search
pubmlst search --contigs contigs.fasta --organism "Escherichia spp."

# rMLST species identification
pubmlst rmlst --contigs contigs.fasta

Outputs

The script writes a summary file (mlst.out or rmlst.out) and server output as a json file.

Reference

Jolley, K. A., Bray, J. E., & Martin. (2017). A RESTful application programming interface for the PubMLST molecular typing and genome databases. Database, 2017. https://doi.org/10.1093/database/bax060

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