No "match_info" field when calling combine_recombinant_info

[hyanwong]

The combine_recombinant_info() function in info.py references a "match_info" field in the metadata, that I don't think exists any more, so the function bombs out. We use this function for saving details of the recombination nodes for plotting.

[jeromekelleher]

The metadata has changed quite a lot, so expect breakage. I'm hoping that the format just-merged is the final one, and we can get stuff sorted out from there.

[jeromekelleher]

For now, please just hack whatever is needed to get results in the short term.

[hyanwong]

In particular, I think I need the "strain" info for recombination node matches, which was previous calculated like:

strain = match_info[0]["strain"]
assert len(match_info) == 2
assert strain == match_info[1]["strain"]

Is that the same as the strain of md["sc2ts"]["hmm"][0]["path"][0]["parent"]?

[hyanwong]

Is that the same as the strain of md["sc2ts"]["hmm"][0]["path"][0]["parent"]?

Hmm, actually, I think the "strain" here is the strain of the node that "caused" this recombination to happen. I'm not sure that's in the metadata now. I'll just set it to None and hope we aren't using it for the plots.

[jeromekelleher]

I think you want causal_strain, yeah. That's in the recombinant summary data frame I'm sure.