This software is for the inference of beta-lactam resistance phenotype from the PBP genotype of Streptococcus pneumoniae.
This software is a modified version of Ben Metcalfe's AMR predictor designed for running within a Docker container, and as part of Pathogenwatch. Please credit the original authors in any resulting publication.
We do not provide any support for the use or interpretation of this software, and it is provided on an "as-is" basis.
In the root directory of the repository run the following command:
docker build --rm -t spn_pbp_amr .
The software reads a FASTA file from STDIN and prints a JSON-formatted result to STDOUT.
cat [path/to/genome.fa] | docker run --rm -i spn_pbp_amr > result.json