Bio-hansel

Latest version: v2.6.1

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2.1.1

* Fix command-line parameter parsing issue 61
* Fix lower-case sequence issue

2.1.0

Changes:

- Adds optional subtype metadata table merging into `biohansel` results
- Name change from `bio_hansel` to `biohansel`

Fixes:

- Change *Salmonella* Enteritidis scheme version to 0.8.0 from 0.7.0
- Shorter more informative QC messages (47)
- MacOS X gzipped FASTA/FASTQ issue (40)
- Fix empty output files when no targets are found in inputs (51)

2.0.0

Changes:

* bio_hansel now only uses Aho-Corasick string searching for finding kmers in sequences using the [`pyahocorasick`](https://github.com/WojciechMula/pyahocorasick/) Python library. NCBI BLAST+ and Jellyfish are no longer needed and have been removed as external dependencies.
* Sorting inconsistent subtypes for QC reporting

Testing:

* Travis CI config simplified; no longer need to download and install Conda since it's now using the Python installation available through Travis CI Linux VMs.

1.3.2

Fixes:

- 35 `ValueError: No objects to concatenate` when no tile results are produced

1.3.1

Adds:
* Version 0.8.0 of Salmonella Enteritidis Scheme.

Fixes:
* Citation fix within the read-me.
* Logo image hosting.

Developer:
* Tests updated for new Enteritidis scheme.

1.3.0

Fixed:
* Fixed disappearing column; Specify only `avg_tile_coverage` to be dropped if null.
* Fixed exp vs obs calculation for missing tiles QC check.

Added:
* Added missing tiles QC check on all inconsistent subtypes found in a result
* Added unit test for getting mixed tile counts method

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