Depicting deletions with plotsr

[ira-zibbu]

Hi,

Long-time user of plotsr, and I enjoy the visualizations it generates. However one feature I have long wanted was to also depict deletions in the synteny plots with a dedicated ribbon. Here I have minimally update the code to enable this.

• Please check if the PR fulfills these requirements

• Is the commit message clear and explains what the PR does?
• Is the PR tested?
• Are tests for the changes available and added (for bug fixes / features)
• If needed, docs have been added / updated (for bug fixes / features)

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

This PR introduces the ability to depict deletions with a dedicated ribbon.

• What is the current behavior? (You can also link to an open issue here)

Currently, deletions are not depicted in the synteny plots.

• What is the new behavior (if this is a feature change)?

Deletion mutations (with the key 'DEL') are depicted with red ribbons. See the following example from two E. coli genomes:

• Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

To the best of my knowledge this should not break the application. The provided test ran successfully.

• Other information:

The main CLI in plotsr.py contains options to disable depicting certain kinds of mutations.

    filtering.add_argument('--nosyn', help='Do not plot syntenic regions', default=False, action='store_true')
    filtering.add_argument('--noinv', help='Do not plot inversions', default=False, action='store_true')
    filtering.add_argument('--notr', help='Do not plot translocations regions', default=False, action='store_true')
    filtering.add_argument('--nodup', help='Do not plot duplications regions', default=False, action='store_true')

I was unable to figure out how these options are used by the script to introduce flexibility in depictions. I propose than an option also be included for deletions, to allow the user to disable depicting deletions if that behaviour is not required.

[lrauschning]

Sorry for the long radio silence, Manish left the lab and plotsr maintenance has been a bit chaotic.
The changes look good, I'll look for a way to get the CLI thing working as well and then merge.

[lrauschning]

Merging, CI on python 3.11 seems to be a bit broken

[lrauschning]

Thanks for the improvement @ira-zibbu :)