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[MRG] use and report ANI from tax genome
summarization
#2005
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Codecov Report
@@ Coverage Diff @@
## latest #2005 +/- ##
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+ Coverage 84.31% 84.34% +0.02%
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Files 130 130
Lines 15293 15320 +27
Branches 2167 2176 +9
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+ Hits 12895 12922 +27
Misses 2095 2095
Partials 303 303
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@ctb I think this is ready for review. Please suggest any additional tests or anything it may need! |
tax genome
summarization?tax genome
summarization?
tax genome
summarization?tax genome
summarization
realized I need to add some docs... will try to do asap :) |
I did a thing, successfully! The following: sourmash gather podar-ref/63.fa.sig gtdb-rs207.genomic-reps.dna.k31.zip
sourmash tax genome --gather-csv 63.x.gtdb.csv --taxonomy-csv gtdb-rs207.taxonomy.csv --ani 0.9 yielded:
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LGTM!
The docs build on my laptop just fine, so I am inclined to merge and then figure out the docs stuff separately. LMK if that's ok.
(starting from #1788)
Add$cANI$ >= threshold, e.g.
--ani-threshold
tosourmash tax genome
, to allow classification based on.95
.Thoughts/warnings:
containment
, because ANI was not yet implemented. I've left containment as the default here, but this might be something we want to change in the future.cANI
has different patterns based on the k-mer size and alphabet (moltype) used. Thresholds should be selected accordingly.