moddotplot - v0.9.8

• Add --region flag to select subsequences #48
• Update documentation images, add sample annotation track.
• Bugfix #31 zero division error for low resolution plots

- Python
Published by alexsweeten 10 months ago

moddotplot - v0.9.7

Bugfix:

• Fixed bug where bedpe file for comparative plots wouldn't link correctly.

- Python
Published by alexsweeten 10 months ago

moddotplot - v0.9.6

Features:

• Adds cooler support for static plots
• Adds a new annotation track for TRI plots (FULL and COMPARATIVE support coming soon!)

- Python
Published by alexsweeten 10 months ago

moddotplot - v0.9.4

New features:

• Parses fasta header when subsequence created using samtools faidx. Moves start and end coordinates to dotplot axes in static mode

Changes: - .bed file output by ModDotPlot changed to .bedpe, to avoid ambiguity with annotation files - Changes --bed to --input in static mode. - --bed now accepts annotation files

- Python
Published by alexsweeten about 1 year ago

moddotplot - v0.9.3

Bugfixes:

• Fixed type comparison bug for when axis need different breakpoint amounts
• Fixed bug preventing comparative histograms from getting output.

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.9.2

Bugfixes: - Fixed bug where file name did not match sequence in comparative mode.

Features: - Added comparative mode sorting feature by size or by order of entry (default).

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.9.1

New features:

• Rasterizes plots by default. Smooths out triangle plots.
• Accepts bgzip compressed fasta files as input

Notes:

• Bug noted in grid orientation: will fix ASAP
• Using -a or -t breaks grid functionality. Will fix ASAP.
• Need to update README with new features

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.9.0

Feature:

• Add grid and grid-only option

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.8.8

Bugfix:

• Fix bug where multifasta files would lose indexing

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.8.7

Bugfix:

• #36 Replace PIL with pillow

- Python
Published by alexsweeten over 1 year ago

moddotplot - v0.8.6

Bugfixes: - #29 Fix axis swap with comparative plots in static mode

Updates: - Update citation file

- Python
Published by alexsweeten almost 2 years ago

moddotplot - v0.8.5

Bugfixes: - #32 fix empty plot when comparing upper v. lower case - Remove sequence size from the x-axis of static plots

Improvements: - plot_TRI is now rotated to be correct orientation

- Python
Published by alexsweeten almost 2 years ago

moddotplot - v0.8.4

Bugfixes: - Fix issue with axes-limits using an incorrect boolean type - Patch for Error when query is shorter than the reference #26

- Python
Published by alexsweeten about 2 years ago

moddotplot - v0.8.3

Bugfix: - Addressed #24

New features: - Axis tick label and size changes for static mode - README updates

- Python
Published by alexsweeten about 2 years ago

moddotplot - v0.8.2

Release notes: - Add citation info 😃 - Patch issue #22 - Minor quality of life updates

- Python
Published by alexsweeten about 2 years ago

moddotplot - v0.8.1

Fixes for #19 and #20, as well a bunch of quality of life updates

- Python
Published by alexsweeten about 2 years ago

moddotplot - v0.8.0

ModDotPlot v0.8.0:

• ModDotPlot must be selected to be run in static mode (moddotplot static)or interactive mode (moddotplot interactive) ahead of time.
• Selecting the number of layers in interactive mode is done by selecting a minimum window size -w. By default, this is set to n/2000.
• Added option to save and load matrices.
• Numerous bugfixes & quality of life updates.

- Python
Published by alexsweeten over 2 years ago

moddotplot - v0.7.2

Minor performance improvements and bugfixes

- Python
Published by alexsweeten over 2 years ago

moddotplot - v0.7.1

Fixes:

• Minor bugfix where running ModDotPlot with config file would error due to unimplemented command line args

- Python
Published by alexsweeten over 2 years ago

moddotplot - v0.7.0

Lots of new features introduced with v0.7.0:

• Interactive mode is now the default. To create static plots, run moddotplot with moddotplot --static.
• Interactive mode now precomputes distance matrices before launching Dash application. Selecting the number of layers to compute can be done with the -l flag.
• Added option to replace command line args with a config file moddotplot -c config to better manage complex customization options. Sample config file. Recommended use for creating static plots.
• Numerous bugfixes & quality of life updates.

- Python
Published by alexsweeten over 2 years ago