Test Data

Test installation

To test that AMRrules is installed and working correctly, test data is included inside tests/data/input/. This includes examples of AMRFinderPlus output files for Escherichia coli and Klebsiella pneumoniae genomes, as well as a multi-species example file.

To run the AMRrules test data, use the following commands:

# test a single E. coli genome (wildtype strain with no acquired resistance phenotypes)
amrrules --input tests/data/input/test_ecoli_wildtype.tsv --output-prefix test_ecoli_wildtype --organism 's__Escherichia coli'

# test a single wild-type K. pneumoniae genome, and flag core genes in the summary output
amrrules --input tests/data/input/test_kpneumo_wildtype.tsv --output-prefix test_kpneumo_wildtype --organism 's__Klebsiella pneumoniae' --flag-core

# test a multi-genome, multi-species example
amrrules  --input tests/data/input/test_multispp_amrfp.tsv --output-prefix test_multispp --organism-file tests/data/input/test_multispp_species.tsv

Outputs will be written to your current working directory, and can be compared to the output files in tests/data/example_output.

Beta-testing data

Additional test datasets are available for select organisms.

Escherichia coli: 20 E. coli genomes ranging from wildtype susceptible to multidrug resistant.

Genomes sourced from Mills et al, 2022, which includes AST profiles available here.

amrrules --input tests/data/input/test_ecoli_20strains.tsv --output-prefix test_ecoli_20strains --organism 's__Escherichia coli'

Klebsiella pneumoniae: 20 K. pneumoniae genomes ranging from wildtype susceptible to multidrug resistant.

Genomes sourced from Heinz et al, 2019, which includes AST profiles available here.

amrrules --input tests/data/input/test_kpneumo_20strains.tsv --output-prefix test_kpneumo_20strains --organism 's__Klebsiella pneumoniae'

Staphylococcus aureus: 20 S. aureus genomes sourced from Worley et al, 2023, which includes AST profiles available here.

amrrules --input tests/data/input/test_saureus_20strains.tsv --output-prefix test_saureus_20strains --organism 's__Staphylococcus aureus'