I am working on using Nextstrain for global surveillance of Influenza. As part of our bioinformatics workflow, we already assign each sequenced virus to a clade (e.g., 3C.2a1b.2a.2) and we can pull this as part of the tabular metadata for a build. Currently
augur clades recomputes this for each node using the definitions file.
Description
I would like to write to a clades.json directly from tabular metadata instead of recomputing the clade based on augur clades.
Examples
Possible solution
1) Function in the API to write an augur formatted json based on tabular data.
2) Logic within augur clades to write the json from strain and clade columns.
Context
I am working on using Nextstrain for global surveillance of Influenza. As part of our bioinformatics workflow, we already assign each sequenced virus to a clade (e.g., 3C.2a1b.2a.2) and we can pull this as part of the tabular metadata for a build. Currently
augur cladesrecomputes this for each node using the definitions file.Description
I would like to write to a
clades.jsondirectly from tabular metadata instead of recomputing the clade based onaugur clades.Examples
Possible solution
1) Function in the API to write an augur formatted json based on tabular data. 2) Logic within
augur cladesto write the json from strain and clade columns.