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* Fixed `KeyError` issue with later versions of pandas (115, thanks javiertognarelli).
* Fix a bug so that the Sequence column in resfinder.tsv uses the isolate sequence instead of the reference sequence
* 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
* Added --output-mlst in Search.py
* Added [coloredlogs](https://pypi.org/project/coloredlogs/) library to format the output * Added support for [MLST](https://github.com/tseemann/mlst)
* 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.
* Add support for scanning against the PlasmidFinder database. * Upgraded the testing package to use [Green test runner](https://github.com/CleanCut/green). * Added Detailed_Summary table which combines results from Resfinder, Pointfinder (optional), and Plasmidfinder. * Added `--ignore-invalid-files` command and check for duplicate sequence ids.
* 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](https://mypy.readthedocs.io).
* 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`.
* Fix issue where `staramr` crashes if an input contig id is a number.
* 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`
* 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).
* Initial release. Supports batch scanning against the ResFinder and PointFinder databases.