0.5.1

• Renamed the following columns for clarification:
  • Plasmid Genes to Plasmid in Summary table.
  • Gene to Plasmid in PlasmidFinder table.
  • Gene to Gene/Plasmid in Detailed Summary table.

0.5.0

• Add support for scanning against the PlasmidFinder database.
• Upgraded the testing package to use Green test runner.
• Added Detailed_Summary table which combines results from Resfinder, Pointfinder (optional), and Plasmidfinder.
• Added --ignore-invalid-files command and check for duplicate sequence ids.

0.4.0

• Add support for campylobacter from PointFinder database.
• Fix read_table deprecation warnings by replacing read_table with read_csv.
• Handling issue with name of 16S gene in PointFinder database for salmonella.
• Refactoring and simplifying some of the git ResFinder/PointFinder database code.
• Added automated type checking with mypy.

0.3.0

• Exclusion of aac(6')-Iaa from results by default. Added ability to override this with --no-exclude-genes or pass a custom list of genes to exclude from results with --exclude-genes-file.

0.2.2

• Fix issue where staramr crashes if an input contig id is a number.

0.2.1

• Minor
  • Updating default ResFinder/PointFinder databases to version from July 2018.
  • Fix regex extracting gene/variant/accession values from ResFinder/PointFinder databases.
  • Fixing a few entries in table mapping genes to phenotypes.
  • Print stderr for errors with makeblastdb

0.2.0

• Major
  • Inclusion of predicted resistances to antimicrobial drugs thanks to gene/drug mappings from the NARMS/CIPARS Molecular Working Group. Resistance predictions are microbiological resistances and not clinical resistances (issue #4, #6).
  • Adding a staramr db restore-default command to restore the default staramr database (issue #3).
  • Switched to using BLAST Tabular data + pandas to read BLAST results (issue #10).
  • Inverted direction of BLAST (we now BLAST the AMR gene files against the input genomes).
• Minor
  • Less verbose messages when encountering errors parsing the command-line options.
  • Able to support adding options after a list of files (e.g., staramr search *.fasta -h will print help docs).
  • Switched to including negative AMR results (samples with no AMR genes) by default. Must now use parameter --exclude-negatives to exclude them (issue #2).
  • Only print 2 decimals in Excel output (issue #5).
  • Automatically adjust Excel cells to better fit text (issue #7).
  • Many other coding improvements (issue #11, #13 and others).

0.1.0

• Initial release. Supports batch scanning against the ResFinder and PointFinder databases.