Pango Lineage code error

[ShaneSchroeder]

I have run into an issue when trying to run PyR0 during the analysis step. The Pango lineages that are checked for in the program here are out of date and crashes because it tries to check a lineage that is not included in their dictionary (e.g. "XAA").

Pango has an updated list here but their dictionary sometimes refers to something like "XAA": ["BA.1","BA.2"] instead of the standard form of something like "L": "B.1.1.10" where a single code corresponds to one specific lineage rather than a list.

The main issue is when it is evaluating a lineage with a code with 3 letters and starts with X (which is required to be evaluated to my understanding), it cannot proceed. This is due to the values for that code being a list that does not refer to any specific lineages but just all sublineages that start with some specific lineage codes.

Traceback for current pango dictionary:

Traceback for updated pango dictionary:

Is there an updated Pango lineage dictionary to use that has specific lineages for the X** codes or is there a plan for an improved pangolin.py version in the future?

[fritzo]

IIRC @bkotzen added some handling of recombinant lineages like this, but I don't know the details.

pyro-cov should download the latests pango dictionary from their github repo, so I suspect this is less an issue with stale dictionaries and more an issue with handling recombination.

[bkotzen]

Right, I believe the issue stems from choosing a parent; I've set up a branch that loads recombinants and randomly chooses one parent to be the designated parent. @ShaneSchroeder try checking out the branch bkotzen-bug-fixes or bkotzen-improvements. I believe recombinants are handled in both those branches.

[ShaneSchroeder]

@fritzo @bkotzen I used pangolin.py from the bkotzen-bug-fixes branch and that has solved my issue, thank you!