predict

acheron predict

Currently supported pathogens are salmonella and campylobacter. Open an issue to request a different one.

acheron predict -m MIC --pathogen salmonella --path "data/genomes/"

acheron predict -m MIC --pathogen campylobacter --path "data/SRR12345.fasta"

The Previous commands will predict antibiotic resistance to either a directory of fasta files or an individual fasta file. The results will be printed to stdout (i.e. to the terminal).

acheron predict -m MIC --path "data/genomes/" -o "abx_predictions.csv"

This command will save the results to a .csv file.

Also supported is .xlsx, .tsv, and .df (pandas pickle). Simply name the file and Acheron will save it in that format.