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WIP: add abund estimation to manysearch
#302
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Comparing this PR's abund Small test dataset:
built and run by @AnneliektH via: https://github.com/AnneliektH/2024-binning-kmer/blob/main/workflow/notebooks/notes_sourmash.ipynb (both run with single thread)
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wow, that's a fantastic speed improvement 😆 |
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Adds abundance columns
average_abund
,median_abund
,std_abund
tomanysearch
output.Changed behavior:
manysearch
to only build & write a result if we find an overlap between the query and search sigs. This was to avoid issues with abundance-related columns (average, median, std deviation calculations), but I think generally this:To Do:
Unfortunately, I can only estimate abundance info from non-rocksdb
manysearch
. Abund estimation for rocksdb databases would require us to estimate these values w/in sourmash, since we don't have access to which hashes match.Note: for
mgmanysearch
type applications, the default threshold, 0.01` is far too stringent. Recommend setting threshold to 0 for these applications.