Changelogs » Staramr

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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
  - --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


* Added [coloredlogs]( library to format the output
  * Added support for [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](
  * 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](


* 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.