8000 Make method to convert a GIG table into a Pandas dataframe · Issue #34 · hyanwong/giglib · GitHub
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Make method to convert a GIG table into a Pandas dataframe #34

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duncanMR opened this issue Oct 17, 2023 · 4 comments · Fixed by #36
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Make method to convert a GIG table into a Pandas dataframe #34

duncanMR opened this issue Oct 17, 2023 · 4 comments · Fixed by #36
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@duncanMR
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While we have a GIG data model, we still lack basic methods to do things like subsetting (e.g. intervals[intervals.parent == 2]) and sorting by a particular column. If we convert a GIG table to a Pandas DataFrame, doing such basic data manipulation is trivial, so I think having such a conversion method available will be useful for exploratory work. It will be hard to do subsetting and sorting more efficiently than Pandas without resorting to the tricks used in tskit, so I'm inclined to kick that down the road for now.
@duncanMR duncanMR self-assigned this Oct 17, 2023
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Yes, we could reasonably use pandas for the moment, as long as we don't end up relying on pandas functions in the scripts we write.

@hyanwong
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A conversion to a pandas dataframe is quite reasonable anyway. FWIW in tsdate, to avoid a pandas dependency we just have an asdict method (or something like that), so you can do df = pd.DataFrame(obj.asdict()), but maybe that's too long a thing to type here, and we just want an obj.df() method?

@duncanMR duncanMR mentioned this issue Oct 17, 2023
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A conversion to a pandas dataframe is quite reasonable anyway. FWIW in tsdate, to avoid a pandas dependency we just have an asdict method (or something like that), so you can do df = pd.DataFrame(obj.asdict()), but maybe that's too long a thing to type here, and we just want an obj.df() method?

I'm inclined to go for the latter for now, since I don't have any use for the dict object outside of turning it into a dataframe. I'm only going to use Pandas in exploratory work, so it won't be any trouble to drop the Pandas dependency later, I think?

@hyanwong
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Sure. Maybe call it obj._df() (with the underscore), to emphasise that it's not part of the public API (not that we actually have one, but nevertheless, a good habit to get into)

@duncanMR duncanMR mentioned this issue Oct 18, 2023
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Add method to convert BaseTable to dataframe duncanMR/GeneticInheritanceGraph
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