augur export case question about augur HOT 3 CLOSED

My suggestion here would be to make sure that deme names in metadata.tsv match deme names in lat_longs.tsv and colors.tsv. I would suggest snake_casing everything in metadata.tsv. This was my standard practice for all other builds.

I want an augur clean module that would take some of the functionality of sacra that would make it easier to get a clean and snake_cased metadata file. Augur clean vs sacra is definitely worth a larger conversation.

In the interim, you could make a simple script to do this if FASTA coming in is capitalized (and has the "non-standard" 2-letter state codes).

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How about converting both the metadata.tsv defined demes and the lat-long demes to lowercase for comparison only, but the exported demes match those in the metadata.tsv?

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Sorry, but I'm worried about that approach. The canonical lat-long file will have names like north_dakota. If metadata comes in as NorthDakota, then simple lowercasing won't work. This particular example would cause some things to match and some to not. It will be opaque on why these are failing. I favor a simple direct comparison. This should make it obvious how to construct lat_longs.tsv.

If someone really doesn't want to use snake_case deme names then they can make a lat-long file with names as NorthDakota etc...

I see now. I was confused.

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