Pygenomeviz

Change Log

Minor Change

- Added `set_sublabel()` method
- Set appropriate matplotlib rc(runtime configuration) params to adjust figure appearence
- Set appropriate GridSpec left-right-bottom-top params to adjust figure appearence
- Used `typing.Literal` to restrict allowed argument values

Change Log

Minor Change

- Added `start_pos` option to `add_feature_track()` method
- Added `position` option to `add_subtrack()` method
- Changed GenomeViz default `plot_size_thr` parameter *0.0005* to *0*
- Changed `add_link()` method to occur error if start-end value is out of track range
- Removed unnecessary `maptype` option of pgv-mummer cli
- Fixed deprecated typing module type hints style (Use built-in types)

Change Log

New Functionality

- Added genome alignment & visualization CLI workflow
- `pgv-mummer`: MUMmer pairwise genome alignment
- `pgv-mmseqs`: MMseqs CDS RBH search in each genome
- `pgv-pmauve`: progressiveMauve multiple genome alignment

- Added MMseqs, progressiveMauve alignment class

Minor Change

- Changed to plot link line if link width is 0
- Added track label color change option
- Changed to manage subtracks independently from other tracks

Change Log

Minor Change

- Improved subtrack add method
- Changed that link track ratios can be set individually
- Added feature label margin (=0.1)

Bug Fix

- Fixed `GC content` & `GC skew` positions misalignment in calculation method
- Fixed incorrect `zero-based` & `one-based` position settings mixture (Unified to zero-based)

First Official Release

pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib.

- Basic functionality implementation is complete
- Still in the development stage