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CHANGELOG.md

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Unreleased

Version 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.

Version 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).

Version 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.

Version 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).

Version 0.7.2.zenodo0

  • Identical code to version 0.7.2 but made mainly to upload this version into Zenodo.
  • Migrated integration tests from TravisCI to GitHub Actions
  • A few small fixes to README.md.

Version 0.7.2

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

Version 0.7.1

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

Version 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

Version 0.6.1

  • Added --output-mlst in Search.py

Version 0.6.0

Version 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.

Version 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.

Version 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.

Version 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.

Version 0.2.2

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

Version 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

Version 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).

Version 0.1.0

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