Refactor MSMS Hits Generation #861
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
update to py311
reconcile main branch updates with feature branch
test: change expected score values for hits refactor
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR will implement major changes to the MSMS hits generation routine, with the objective of simplifying the codebase and improving efficiency. Custom spectral alignment and scoring code has been replaced with MatchMS and the hits generation routine has been restructured to avoid extensive iteration. With these changes, the average experiment should have a ~6X speed increase to hits generation. This will allow for the analysis of much larger experiments or the use of larger atlases.
Custom code is still present for aligning spectra used in plotting MSMS mirror plots. Extensive docstrings have been added to some of the more esoteric functions that accomplish this.