Releases · phac-nml/staramr

Updated the Plasmidfinder database to use the January 18th 2023 release.
Fixed an issue where the string "None" in the drug table would be parsed differently by different versions of pandas (#175).
Upgraded to pandas version 2.
Added the CGE-predicted phenotypes, PMID, Mechanism, and the Required Mutation columns to the Pointfinder output.
The resfinder.tsv and pointfinder.tsv outputs now contain a Notes column.
Updated the help description of the --mlst-scheme parameter to include a more useful link for available schemas.
Switched to only officially supporting Python 3.7+ due to recent incompatibilities with Python 3.6 and some Python packages (numpy, biopython, and others).
Adds the ability to handle "complex" pbp5 mutations. When appriopriate many pbp5 point mutations will be reported as a single mutation.
Resfinder CGE-predicted phenotypes are now reported in the summary and detailed summary alongside existing predictions.
Corrected a typo in the position for acrB in the PointFinder drug key table.
Removed "enterobacteriaceae" from the list of supported PlasmindFinder databases.
Changed the word sensitive to susceptible in outputs.

Updates to PointFinder database handling
- Adds the ability to handle promoters (regions with both promoter nucleotide information and non-promoter codon information)
- Adds handling of insertions and deletions in nucleotide and codon sequence
- Updates list of supported PointFinder species to salmonella, campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori.
Switch name e.coli to escherichia_coli in PointFinder gene-drug key to match organism name in PointFinder database.

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