Testing related topic to domibubble

[ASLeonard]

Hey Erik,

I was looking at this because bubble gun did not seem to produce sensible bubbles from pggb output. I used a lot of networkx in a previous life, so figured I would just use their strongly connected component algorithm since that is what you were using here.

I can't believe it seems to work, but just changing nx.MultiGraph to nx.DiGraph in pygfa and then finding SCCs actually worked out the box (and only used ~5 Gb and 1 CPU hour for one 100 Mb chromosome with 8 assemblies). Analysing bubbles seems like it will be a common op soon, so just wanted to share that this worked in case it is of any help.

This is a subgraph with gray nodes and recolouring the two SCCs pink and blue.

Best,
Alex