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consider providing standardized parameter files/-P for sourmash sketch #1910

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ctb opened this issue Mar 30, 2022 · 0 comments
Open

consider providing standardized parameter files/-P for sourmash sketch #1910

ctb opened this issue Mar 30, 2022 · 0 comments

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@ctb
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ctb commented Mar 30, 2022

The goal would be to be able to encode collections of parameter strings in a file, to pass into sourmash sketch commands.

per Luiz comment, probably something in TOML:

may I suggest toml instead of YAML? It would look something like this:

[[MinHashSpec.dna]]
ksize = [ 21, 31, 51 ]
scaled = 1_000

[[MinHashSpec.protein]]
input = [ "dna", "protein" ]
ksize = 10
scaled = [ 100, 200 ]

[[MinHashSpec.dayhoff]]
ksize = 16

Many places (including Python with pyproject.toml) are moving away from YAML because it has some confusing parsing issues (due to being underspecified).

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