Track down inefficiency in database parsimony within MetaMorpheus...

smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

https://smith-chem-wisc.github.io/Spritz/

MIT License

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Track down inefficiency in database parsimony within MetaMorpheus... #147

Closed acesnik closed 4 years ago

acesnik commented 5 years ago

Search of 18 fractions without pruning finished easily
GPTMD of 18 fractions finished easily
Search of 18 fractions with pruning didn't finish... is this because of the code for pruning sequence variant modifications?

Here's the database to test and a diagnostic session for what I'm seeing. "\bison\share\Projects\Spritz\SlowParsimonyWithLotsOfMods"

acesnik commented 5 years ago

It turns out this is from parsimony, rather than pruning. The LINQ command .First() accounts for 40% of the computation during parsimony with lots of mods. I'm not sure how to fix that.

acesnik commented 5 years ago

This looks like a hotspot https://github.com/smith-chem-wisc/MetaMorpheus/blob/master/EngineLayer/ProteinParsimony/ProteinParsimonyEngine.cs#L151

But it depends on the ordering in BestMatchingPeptides, and that's mystifying.

acesnik commented 4 years ago

This was resolved somewhere along the road.