[MRG] add some docs on search, gather, and lca methods #393
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ctb
changed the title
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Ready for review & merge, @brooksph @taylorreiter @luizirber. While this is incomplete, it is a massive upgrade to the current documentation :). I'd like to suggest that review focus on accuracy, and that suggestions for the next round of improvement get added to a new issue. That way we can merge this sooner rather than later, while also keeping track of ideas for future improvements. |
doc/classifying-signatures.md
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| We have implemented two algorithms in sourmash to do this. | ||
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| One, approaches based on lowest common ancestor ("LCA"), uses |
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The language here is a little confusing, but not that critical to change
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Fixed! Thanks for noticing!
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| By default, there is no structured taxonomic information available in | ||
| sourmash signatures or SBT databases of signatures. Generally what | ||
| this means is that you will have to provide your own mapping from a |
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Does this refer to the output of gather? (Line 72-74)
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No, it refers to all of the non-LCA stuff. This is just going to have to be confusing, given the addition of lca gather :).
| `gather`, like `search`, will load all of provided signatures into | ||
| memory. You can use `sourmash index` to create a Sequence Bloom Tree | ||
| (SBT) that can be quickly searched on disk; this is | ||
| [the same format in which we provide GenBank and other databases](databases.html). |
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Line 205-207 is repeated above. I see the utility of the information being in both places, but is it repeated verbatim intentionally?
doc/command-line.md
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| These commands use LCA databases (created with `index`, below, or | ||
| prepared databases such as | ||
| [genbank-k31.lca.json.gz, from the LCA tutorial](tutorials-lca.html). | ||
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I thought index was to create the SBT for gather?
doc/command-line.md
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| ### `sourmash lca gather` | ||
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| The `sourmash lca gather` command classifies finds all non-overlapping |
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classifies finds -- too many words I think
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@taylorreiter fixed in b10b490 - thx! |
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yay thanks! ...do you think we should wait for #390 to merge? I'm -0 on waiting. |
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(because this includes docs for |
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I don't have strong feelings either way, or a strong concept of the number of people we will confuse by merging now as opposed to waiting. |
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On Sun, Feb 18, 2018 at 10:20:29AM -0800, Taylor Reiter wrote:
I don't have strong feelings either way, or a strong concept of the number of people we will confuse by merging now as opposed to waiting.
yeah, me neither. Heck, I'll just merge it.
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Update documentation significantly in preparation for 2.0 release -
Note, includes documentation for
lca gather, introduced in #390. Incorporates PR #362 as well.make testDid it pass the tests?make coverageIs the new code covered?without a major version increment. Changing file formats also requires a
major version number increment.
changes were made?