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sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.
http://sourmash.readthedocs.io/en/latest/
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support outputting manifests or manifest-like files as direct `-o` output. #1902

Open ctb opened 2 years ago

ctb commented 2 years ago

In #1493, we added sourmash_args.SaveSignaturesToLocation(...) to support a wide variety of output formats.

In #1891, we are adding the ability to read manifest files, as output by sourmash sig manifest.

Per the motivation in https://github.com/sourmash-bio/sourmash/issues/1365, it would be nice to be able to output these manifest files as the result of searches etc. -o could maybe support that, under certain conditions - in particular, that all signatures were loaded from identifiable locations (so, not stdin; anything else?)

One concern is that these manifest files would not necessarily be that portable or relocatable, depending on whether they contained relative paths or abspaths - both are problems. So it could be a buyer-beware kind of situation to support @bluegenes -like people, that is, expert users.

ctb commented 2 years ago

in #1891, I'm adding sourmash sig check --output-manifest-matching which will output entries that match to a picklist in manifest format. Right now it's specific to this command, but we'll be using it for https://github.com/sourmash-bio/sourmash/issues/1671 so if it proves out there we can revisit and implement more broadly.

ctb commented 8 months ago

note to self - we could implement this as a save plugin pretty easily.