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Provide a standard selector for signatures based on md5sums #599

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ctb opened this issue Jan 4, 2019 · 3 comments
Closed

Provide a standard selector for signatures based on md5sums #599

ctb opened this issue Jan 4, 2019 · 3 comments

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@ctb
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ctb commented Jan 4, 2019

We could usefully generalize parts of the command line interface (and underlying Python API) to widely support the use of md5sum selectors for signatures.

As of #587 we have added sourmash signature extract which takes -md5 <substring> as an optional argument. Many commands already take k-mer size -k and moltype --dna/--protein selectors to specify distinct/unique signatures, and this is (in particular) supported in the Python API with load_one_signature. Perhaps we can generalize this, and clearly distinguish between load_one_signature and load_signatures commands, where the latter would only take signature compatibility arguments (ksize, moltype) and the former could take md5sum and other things?

For example, sourmash gather and search could look like:

sourmash search foo.sig database.json --query-md5=a3531f53

OR (more compact, less friendly?)

sourmash search foo.sig:a3531f53 database.json

this idea needs fleshing out and Python API level support, of course.

This is an update of #239.

Also see #594 which would suggest that we want to be able to provide this kind of selector to pull query sigs out of databases, too.

@ctb
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ctb commented Jan 14, 2019

might be nice to provide a way to select collections of signatures based on selectors in files (md5sums, or something else). or maybe too much?

@ctb
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ctb commented Jun 28, 2020

#1059 adds this functionality to load_query_signature.

@ctb
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ctb commented Jul 2, 2020

#1072 is better and more general, closing in favor of that issue.

@ctb ctb closed this as completed Jul 2, 2020
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