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tutorial-lin-taxonomy.html contains links to data sets that are not in the sourmash-bio repository. tsk tsk. 😁
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So! good news for those of us trying to distribute files! per e-mail (copied below) `~/public_html/` is exposed and supports symlinks, too!
so if you want to expose files, do
```
mkdir ~/public_h…
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For the taxonomy filtering script that's the default action right now, `just_taxonomy.py`, the pipeline does its own database search to determine taxonomy by looking at the majority LCA match. If it c…
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The `MultiIndex` class is used for four purposes:
* loading one or more signatures from JSON via stdin
* loading one or more signatures from a JSON file
* loading one or more .sig/.sig.gz files fro…
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SBT allows repeatedly inserting the same leaf:
``` python
from sourmash_lib.sbt import SBT, GraphFactory
from sourmash_lib.sbtmh import SigLeaf
from sourmash_lib import signature
sig = next(sig…
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Discussion in https://github.com/sourmash-bio/sourmash/pull/2178 reminded me of some things @ctb and I talked around a while back, and that seem like far less of a leap now.
With new selection and …
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per #307, "PyO3 0.21.0 - This release introduces a substantial new direction for PyO3's API".
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We are getting closer to being able to separate out the lineage stuff from the revindex stuff in LCA, so we could envision combining searches on signatures and SBTs with taxonomic reporting (where ava…
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Hello,
In running `sourmash compare` on ~300k genes with scaled=10, I kept running into both out of memory (bus error: core dumped) and `no space left on device` errors, and I think the way to fix t…
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Hi! 👋
I was going to install genome-grist and spacegraphcats into one conda environment.
I started by doing a fresh install of genome-grist, and then when I went to install spacegraphcats, I got a…