staramr - 0.11.0

• Updated the Resfinder database to use the 2024-08-06 release (#217).
• Updated the Pointfinder database to use the 2024-08-08 release (#217).
• The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: pmrA -> pmrA_1_CP055130.1). StarAMR has been updated to support this, but database backwards compatibility is unlikely.
• The genes_to_exclude is affected by the above change and must now use gene IDs that exactly match the new FASTA record IDs with accession IDs.
• Removed ARG drug key entries with "None" or missing resistance (#218).

- Python
Published by emarinier over 1 year ago

staramr - 0.10.0

• 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.

- Python
Published by apetkau almost 3 years ago

staramr - 0.9.1

• Fixed a bug that occured when parsing some plasmid FASTA record IDs (PR 159).
• Fixed issue where sometimes the extraction of error messages from makeblastdb was crashing leading to less useful errors (PR 160).

- Python
Published by apetkau over 3 years ago

staramr - 0.9.0

• 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.

- Python
Published by apetkau over 3 years ago

staramr - 0.8.0

• Fixed issue when using older version of pandas (#136) (0.8.0.dev0).
• Fixed up some Python warnings related to pandas (0.8.0.dev0).
• Adjusted mlst tests to account for differences in results for newer versions (0.8.0.dev0).
• Drop support for Python 3.5 as it leads to issues with managing dependency versions (0.8.0.dev0).
• Switched from disallowing to generating a warning when the PointFinder organism is not one of the validated organisms (0.8.0.dev1).
• Updated ResFinder and PointFinder gene drug key to 072621 (0.8.0.dev2).
• Updated default database commits to those corresponding to dates used by ResFinder (2022-05-24), PointFinder (2021-02-01), and PlasmidFinder (2021-11-29) (0.8.0.dev2).
• Fixed issue when multiple matches for same amino acid change to try and select the most specific amino acid change (0.8.0.dev2).
• Fixed up PlasmidFinder database handling to account for changes to PlasmidFinder database structure (0.8.0.dev2).

- Python
Published by apetkau about 4 years ago

staramr - Re-release of 0.7.2 for Zenodo

The code for this release is identical to 0.7.2 but is being re-released so it automatically integrates into Zenodo.

There are a few non-code changes:

• Continuous integration tests have been migrated from TravisCI to GitHub Actions
• README.md has been updated to include more detailed installation instructions.

- Python
Published by apetkau over 4 years ago

staramr - 0.7.2

• Fixed KeyError issue with later versions of pandas (#115, thanks @javiertognarelli).

- Python
Published by apetkau over 5 years ago

staramr -

• Fix a bug so that the Sequence column in resfinder.tsv uses the isolate sequence instead of the reference sequence

- Python
Published by Takadonet over 6 years ago

staramr - 0.7.0

• Added quality module that adds PASS/Fail column and detail information in Summary.tsv
• Added following new optional arguments for Search.py
  • --genome-size-lower-bound
  • --genome-size-upper-bound
  • --minimum-N50-value
  • --minimum-contig-length
  • --unacceptable-number-contigs
• Add DNA column in Resfinder report

- Python
Published by Takadonet over 6 years ago

staramr - 0.6.1

• Added --output-mlst in Search.py

- Python
Published by apetkau over 6 years ago

staramr - 0.6.0

• Added coloredlogs library to format the output
• Added support for MLST

- Python
Published by apetkau over 6 years ago

staramr -

• 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.

- Python
Published by apetkau about 7 years ago

staramr -

• 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.

- Python
Published by apetkau about 7 years ago

staramr -

• 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.

- Python
Published by apetkau over 7 years ago

staramr -

• 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.

- Python
Published by apetkau over 7 years ago

staramr -

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

- Python
Published by apetkau almost 8 years ago

staramr -

• 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

- Python
Published by apetkau almost 8 years ago

staramr -

• 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).

- Python
Published by apetkau almost 8 years ago

staramr -

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

- Python
Published by apetkau about 8 years ago