genbank support, stacked contigs, etc.

[seanrjohnson]

Hi David, I really like your genomenotebook project. Just wanted to let you know that I've been working on adding a bunch of features to it. The purpose is so that it can be used to compare stacks of genome neighborhoods, for example from metagenomic contigs.

Specifically, I'd like to add support:

• genbank file input
• stacked contigs
  • For example, with a shared x-axis.
• stacked features within each contig
• custom colors for each annotation
• various improvements to mouseovers
• allow different annotations and names for different feature types
• export to .html file
• write names on top of feature glyphs (will make stacked features look better)
  • I think this will be the trickiest part, because of needing to turn on and off names based on zoom level.
• clean up the way that annotations and mouseovers are handled

Probably some other stuff that isn't coming to mind right now. It's looking like most of that stuff can be added without breaking backwards compatibility. I've gotten a good start on it, but still have some work to do. Hopefully some or all of it can be integrated back into the main repo eventually.

My branch is here: https://github.com/seanrjohnson/genomenotebook/tree/genbank

The diff for a recent commit is here: https://github.com/seanrjohnson/genomenotebook/commit/ac762887bd4c87e0a14d455199810bd8a38a0381

A jupyter notebook with a demo of some of the stuff is here: https://github.com/seanrjohnson/genomenotebook/blob/genbank/nbs/03_Stacking.ipynb

I'd be happy to hear your thoughts on any of this,

Sean

[seanrjohnson]

I made a bunch more updates to my fork. Let me know if you want to integrate some or all of this into the main repository and I'll try to help with it. Otherwise I'll just maintain mine as a separate fork.

https://github.com/seanrjohnson/genomenotebook/tree/genbank

[dbikard]

Hi Sean, it's great to see that you've been adding new features!!! I'm just getting back from vacation and I will need a bit of time to put my head back into this. I'll try to understand the changes you've made and I'll get back to you if I have any questions. Best, David

On Sat, Aug 19, 2023 at 12:34 AM Sean @.***> wrote:

I made a bunch more updates to my fork. Let me know if you want to integrate some or all of this into the main repository and I'll try to help with it. Otherwise I'll just maintain mine as a separate fork.

https://github.com/seanrjohnson/genomenotebook/tree/genbank

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-- David Bikard