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ENH: Allow specification of node_data key that augur clades outputs #1027

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LauraU123 opened this issue Aug 19, 2022 · 2 comments
Open

ENH: Allow specification of node_data key that augur clades outputs #1027

LauraU123 opened this issue Aug 19, 2022 · 2 comments
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enhancement New feature or request

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@LauraU123
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Sometimes one wants to use multiple independent clade systems, like clade, outbreak, lineage in monkeypox or whole genome clade and G gene clade in RSV

Right now, augur clades always outputs a node data json with a magic fixed key clade_membership.

It would be nice if one could optionally adjust this key name through a CLI argument to augur clades.

That would save a lot of sed commands that are necessary otherwise in multiple scripts.

@LauraU123 LauraU123 added the enhancement New feature or request label Aug 19, 2022
@tsibley
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tsibley commented Aug 23, 2022

Making this adjustable makes sense to me. There's a few places in Augur and Auspice which special-case the clade_membership field. We'd potentially want to make the special-cased behaviour also apply to augur clades output that used other field names.

@jameshadfield
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This should be solved shortly with the merge of #728. This will allow you to specify the key for nodes which belong to the clade via --membership-name as well as setting a custom branch label name for the clade via --label-name.

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