Rewrite reclustering #340
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Rewrite reclustering #340
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jakobnissen
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Needs benchmark
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Hm, it may be that the changed deduplication is actually worse - perhaps because most contigs have no marker information, so this new approach that dynamically finds the best clusters is not as good as globally finding the best eps value, allowing the clusters with markers to inform the eps value of the clusters without markers. Needs tests. |
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This commit makes parsemarkers work even when the split contigs do not have integer identifiers. It also allows easier subsetting of the contigs to predict genes for. The API is still a little bad, but it's being restricted by Python's bad multiprocessing.
This commit completely rewrites reclustering. A few important differences: * It now uses Markers from vamb.parsemarkers, avoiding shelling out to prodigal and hmmer * The algorithm used to pick the best disjoint bins in the DBScan algorithm is faster, and should also produce better results. * The code is almost completely statically analyzable * Pandas is no longer used
Commit cb93655 removed the last use of Pandas in the codebase. Good riddance!
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I'm going to merge this and then commence the larger quality control and testing needed for v5. That implies there will probably be some bugs in this commit. |
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This PR completely rewrites reclustering. A few important differences:
and hmmer
faster, and should also produce better results.
It also refactors
parsemarkers.py.It is built on #339, so that needs to be merged first.
TODO