A simple python wrapper for querying sequences on PubMLST via RESTful API.
Python3 on the path and requests module are required to run pubmlst script.
sudo apt-get install python3-requests
or
pip install requests
# list available MLST organisms
pubmlst list
# ST search
pubmlst search --contigs contigs.fasta --organism "Escherichia spp."
# rMLST species identification
pubmlst rmlst --contigs contigs.fasta
The script writes a summary file (mlst.out or rmlst.out) and server output as a json file.
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