DMS view

[wsdewitt]

This PR adds a directory dms-view/ with assets for populating the dms-view browser. The readme in this directory describes the details.

Notes:

• There is currently a standalone jupyter notebook to generate the dms-view data using DMS data in the results/ directory, but this could be integrated into the main snakemake pipeline if desired.
• It might be more appropriate for the PDB file to live in the main data/ directory?
• The markdown description file has placeholder text that needs updating with info about the CryoEM structure.

[tylernstarr]

Thanks for putting this together @wsdewitt !

I agree, it would be nice if the files were auto-updated as part of the snakemake pipeline? At the same time, it seems like the DMS data is likely stable at this point, so it's probably not hugely important.

I would say the pdb location works for now -- I will eventually make a "split" pdb for mapping DMS data to pdb for Pymol-rendered views. What I mean by that, is there are two sets of mAb:CGG pairs in this pdb, so there are more chains than are needed in teh dms-view build. When I do make this updated pdb, I will put it in the base ~/data folder, and also give it a name in the config.yml.

I'll let you do the final merge as I suspect you'll have to quickly update the dms-view file pointers when the files move from branch to main.

[wsdewitt]

Thanks @tylernstarr! Another complication is that I've recently added info from the gcreplay data (i.e. mutation incidence in the trees) to the notebook that creates the data frame for dms-view, so now there's a dependency on data in that (currently private) repo. It might be best to keep this PR open for now, and maybe we'll eventually migrate the dms-view folder to the gcreplay repo when that is publicly accessible. Let me know when you've modified the pdb, and I can work on updating the dms-view notebook.

I think the todos are:

• PDB update
• update links to gcreplay repo when public (and maybe migrate dms-view there)
• merge PR, and update dms-view links to point to files on main branch