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WIP: use identical column names as sourmash gather #259

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bluegenes
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@bluegenes bluegenes commented Feb 29, 2024

It came up in discussions for #234 that we should try to keep column names the same as in base sourmash.

This PR updates column names from rocksdb fastmultigather so that they match sourmash gather.

  • match_name --> name
  • match_md5 --> md5
  • match_filename --> filename

I'd love for us to update these in sourmash gather at some point, but this is not really the place to do that.

@ctb
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ctb commented Feb 29, 2024

dangit, taking me at my word and all...

We could standardize on the prefetch column names, which I think make a lot of sense.

@bluegenes
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bluegenes commented Feb 29, 2024

We could standardize on the prefetch column names, which I think make a lot of sense.

prefetch cols, from https://github.com/sourmash-bio/sourmash/blob/latest/src/sourmash/search.py#L366C5-L390C26:

prefetch_write_cols = [
"intersect_bp",
"jaccard",
"max_containment",
"f_query_match",
"f_match_query",
"match_filename",
"match_name",
"match_md5",
"match_bp",
"query_filename",
"query_name",
"query_md5",
"query_bp",
"ksize",
"moltype",
"scaled",
"query_n_hashes",
"query_abundance",
"query_containment_ani",
"match_containment_ani",
"average_containment_ani",
"max_containment_ani",
"potential_false_negative",
] #'match_abundance'

Sure. This introduces a minor annoyance, though: any gather <--> fastmultigather file comparisons will need to account for this name difference.

@ctb
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ctb commented Feb 29, 2024

true. But, eventually, we will move the fields over to the prefetch names as much as possible, per sourmash-bio/sourmash#1555

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okay! i shall close :)

@bluegenes bluegenes closed this Feb 29, 2024
@bluegenes bluegenes deleted the harmonize-names-with-sourmash branch March 6, 2024 20:15
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2 participants