v0.5.0

This release add a new --version option which print the version number of the package.

Minor changes to parameter handling.

v0.4.1

This release provides updates to the v0.4.0 release that could not be made
available on pypi because of outdated package metadata and formats

• Fixes and modernizes metadat and package structure

• Add new options to OMArk (via 0.4.0):

  • Option -n/--min_n_species: allow users to chose the minimal number of representative species needed in the OMA database for selecting an ancestral clade (default:5)
  • Option -s/--summarize_db : standalone option to create a summary of the available lineage in the OMAmer database
  • Change in memory access that result in computational efficiency gains, at the cost of increased RAM usage.

Full Changelog: v0.4.0...v0.4.1

v0.4.0

Add new options to OMArk:

• Option -n/--min_n_species : allow users to chose the minimal number of representative species needed in the OMA database for selecting an ancestral clade (default:5)
• Option -s/--summarize_db : standalone option to create a summary of the available lineage in the OMAmer database
• Change in memory access that result in computational efficiency gains, at the cost of increased RAM usage.

v0.3.1

• Added an option to use a local ete3 database for access to the NCBI taxonomy
• Added better handling of taxonomic rank selection, which can now chose the closest rank when the one selected is not available in the OMAmer database
• Added new file checks to make sure the files provided by an user are compatible, and exit cleanly if not

v0.3.0

New OMArk version compatible with OMAmer v 2.0.0.

Changes are:

• Due to changes in OMAmer, dubious proteins or proteins with no homologs now will tend to be placed as Unknown rather than Inconsistent.
• Slight changes to contamination detection module that account only for most significant hits and handle better close contaminants.
• Adding -r option that allows to gives a taxonomic rank as parameter (order, class, phylum) for ancestra lineage selection.
• Adding a warning when the clade chosen is subgenus or phylum and higher.
• Adding the -c options that only outputs a list of conserved HOGs for a given clade.
• Adding a new companion Notebook to contextualize OMArk results with OMA data (sequences, synteny).
• Adding new simulation for benchmarking (genome_simulation.py)
• Minor fix to setup.cfg and import of the Bio library

v0.2.5

• Fixed an issue (Reported in #13) where OMArk was assuming the OMAmer database was issued from a complete main OMA release and was throwing errors when using other databases (Example: Metazoa.h5 ).
• Updated and fixed typos in the README
• Fixed a minor typo in the graphical output

v0.2.4

-Fixes a compatibilty issue with matplotlib on newer versions and newer python, that enforces linewidth argument to be numeric.

v0.2.3

• Added a companion script and a Jupyter Notebook to allow for vizualisation of multiple results on a single figure
• Fixed typos in Readme
• handle filenames that contain '.sum' in the middle of their filename
• update github action versions

v0.2.2

Full Changelog:

• fixes an issue with that matplotlib on newer versions and newer python enforces linewidth argument to be numeric

v0.2.1

-Changed color schemes of figures
-Minor fix to contamination detection module