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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:
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 withload_one_signature
. Perhaps we can generalize this, and clearly distinguish betweenload_one_signature
andload_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
andsearch
could look like:OR (more compact, less friendly?)
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.
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