Hello, I have already carried out several tests with the pipeline and I have very interesting results, I see how in my analysis the transmission between 1 point and another seems to be different and I would like to have a numerical data to compare them. Is there any way to get this value? I’ve searched through the files in the results folder but none seem to suit my need.
Thank you
David
Hi David,
What is the pipeline you are using?
the transmission between 1 point and another seems to be different and I would like to have a numerical data to compare them.
I’m not sure I understand what you mean by different. Do you mean the number of transmission lines coming out of each location?
If so, I believe the transmission lines in Auspice are determined by the output JSON file from augur export v2 --output. Specifically, the recursive property of tree.properties.children determines where transmission lines go.
Take for example the ncov open reference dataset which is created from this JSON file, a relatively small file with ~200 samples. You could read the JSON file in a script, parse it to recursively go through the tree samples (nodes), and get a count of the number of children at each node. Note that there may be multiple nodes at a location, so you should also parse each node’s node_attrs.<geo_resolution>.value and use that to get number of transmissions from each location.
Best,
Victor
Hello, thanks for answering
It’s just as you mention
Do you know if my question has anything to do with the mugration_model.txt file?
Regarding the script, I do not master the subject, I suppose I will have to learn to use it
Hi David,
I’m not familiar with that file, but it has been referenced a few times in this discussion forum, as you have seen:
Based on the documents linked in (1), it seems to be related on the subject of transmissions between locations. However, looking at the file contents pasted in (2), I don’t know how to get the number of transmissions from the matrix rates, or if that is even possible.
If you are looking to get the number of transmission lines, I recommend the approach I outlined in the last paragraph of my reply above. If you haven’t written a script like this before, I suggest using Python and the json library.
Best,
Victor