Export transmission lines

General
1

Hi,

I performed an analysis of Armenian sequences along with ~ 9000 background sequences. In auspice I have transmission lines visualization, however, I would like to export them for every clade and lineage. For example, I see B.1.1.163 transmission from Russia to Armenia around September 2020.
Is there a way to obtain a spreadsheet where I will have “from country” “to country” “lineage”, “clade”, “date” columns?

Any help is greatly appreciated.

Sincerely,

Arsen

2

To get this information you’ll have to parse this out of the dataset JSON or the node-data JSON produced from augur traits. Something like the following should work

# pseudocode
def recurse(node, parentState=None):
    state = node.get("node_attrs", {}).get("country", {}).get("value", None)
    if state and parentState and state != parentState:
        print(f"Transition from {parentState} to {state}")
    for child in node.get("children", []):
        recurse(child, state)

recurse(jsonContents["tree"])
3

Dear james,

Thank you very much.

Sincerely,

Arsen

4

Hi James,
I am trying to export similar data as in the above query (to and from data etc.) something similar to how the old mesquite and MacClade programs give out a migration matrix. Could you please help with how I can extract that information from the traits json/traits.mugration_model.txt.
Thanks,
LC

5

I’m not familiar with the format of mesquite / MacClade, but the *.mugration_model.txt has the migration matrix you’re after. For instance, here’s the output from the zika tutorial:

Map from character to field name
A:	North America
B:	Oceania
C:	South America
D:	Southeast Asia
E:	?


Substitution rate (mu): 97.422118

Equilibrium frequencies (pi_i):
  A: 0.3149
  B: 0.2451
  C: 0.2159
  D: 0.2241

Symmetrized rates from j->i (W_ij):
	A	B	C	D
  A	0	0.8828	2.7937	0.8633
  B	0.8828	0	1.2785	1.3023
  C	2.7937	1.2785	0	0.8635
  D	0.8633	1.3023	0.8635	0

Actual rates from j->i (Q_ij):
	A	B	C	D
  A	0	0.278	0.8798	0.2719
  B	0.2164	0	0.3133	0.3192
  C	0.6033	0.2761	0	0.1865
  D	0.1934	0.2918	0.1935	0