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add additional summary types to vars/vars_to_string.py #7

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rjchallis opened this issue Jun 15, 2022 · 2 comments
Open

add additional summary types to vars/vars_to_string.py #7

rjchallis opened this issue Jun 15, 2022 · 2 comments

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@rjchallis
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rjchallis commented Jun 15, 2022

e.g. range(), length()

@Euphrasiologist
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@rjchallis where are these summary types defined? I can see stuff like this in the result fields JSON:

"summary": [
                "primary",
                "median",
                "min",
                "max"
            ]

But some only have median e.g. mitochondrion_assembly_span, and gc_percent only has "summary": "median",. Is this because bits haven't been implemented, or for data limitation reasons?

I can't see range anywhere yet (is that to be implemented?). I'm looking to update the parsing on the little python script in the vars directory to list all the associated summary functions, and re-do some of the parsing in the expression.rs file.

@rjchallis
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These are defined in the import YAML, then recorded in the attributes index and available via resultFields as you have found. Range is supported, but isn't currently being used for any variables - you'll need to ask over at goat-data to see if there are plans to use it. Similarly decisions on which summary to use are made by the curators for each attribute so some have more values available than others

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