functionality re: lineages that match but have addl taxonomic detail? #1027
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@@ Coverage Diff @@
## lca_summarize_weighted #1027 +/- ##
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- Coverage 92.34% 92.01% -0.34%
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Files 72 72
Lines 5446 5446
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- Hits 5029 5011 -18
- Misses 417 435 +18
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nice tests! I love this way of asking questions 😂 this is based on my understanding of how kraken does things; see the first figure in http://ivory.idyll.org/blog/2020-sourmash-gtdb-oddities.html, where the leaf node for the highest weighted path is the one that is used. See the make_lca code for details - it builds the LCA based on branching paths in the tree. I added an explicit new test in e13d34c to make it clear that this is intentional behavior from make_lca. |
* an initial refactoring to pass abundance weighting around * add exception to flag non-flattned signatures * some tests for --with-abundance * add new test module for lca functions specifically * some tests for abund behavior. conflicted about results. * weight hashvals properly * fix lca summarize tests * revise commentary * put counting in original count_lca_for_assignments * revert a lot of the original changes to command_summarize :) * all tests working * add a test for --with-abundance with real data * fix calculation of total hashvals to get ratios working properly * fixin' the tests * add tests for a fake set of abundances (constructed/simulated) * update summarize docs * adjust language * added and tested output messages * functionality re: lineages that match but have addl taxonomic detail? (#1027) * add test * simpler test to showcase * improve test decription * comments & add test Co-authored-by: C. Titus Brown <[email protected]> Co-authored-by: Tessa Pierce <[email protected]>
So, I hadn't thought much about gather and needed to wrap my head around the gather_assignments functionality when lineages match, but one is more detailed:
We keep the more detailed info, so
a;b;d+a;b;d;eyieldsa;b;d;eThis makes decent sense to me, as we always want to gather the best matches, and can summarize up later. But it's a little unintuitive to me that the count of
a;b;dis 0 (abund test 4).@ctb can you explain pls?