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marbl / MetagenomeScope

Visualization tool for (meta)genome assembly graphs
https://marbl.github.io/MetagenomeScope/
GNU General Public License v3.0
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Detect paths encoded in GFA files and pass to user interface #208

Closed fedarko closed 1 year ago

fedarko commented 3 years ago

Offshoot of #147. Will depend on #205 being merged in.

The idea here is taking these paths (called "paths" in GFA1, still called "paths" but encoded as O-lines (ordered "groups") in GFA2) from an input GFA file and storing them so that they can be viewed in the interface analogously to how paths in AGP files can be viewed. Fortunately, getting paths from GfaPy seems pretty simple (just using g.paths), so the main challenge will just be passing this data to the JS cleanly (and figuring out how to represent it -- should this be independent of the AGP visualization? an alternate set of widgets?)

U-lines (unordered "groups") in GFA2 files might also be usable in the same way, but I suspect that might not be worth the trouble -- the interpretation seems different. Can reevaluate if there is demand.

It would be great to make this very simple for users, but in the worst case scenario (passing the path info is challenging) it should be pretty doable to write some code that converts the paths in a GFA file to AGP, which users can then upload in the interface.

fedarko commented 1 year ago

Coming back to this; since this is a subset of #147, I'm closing it so that I can centralize work on this there.