Open
Conversation
|
|
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
This PR implements a batched OpenKnot score which can be used to parallelize scoring of multiple RNA chemical mapping data samples (1 sample = 1 readout for 1 RNA sequence) to a target secondary structure with pseudoknots. Batched score is significantly faster.
Implementation Notes
@luxaritas Please feel free to suggest changes before merging. I think the OK scoring pipeline had received some updates (e.g. no longer using some global variables and a different set of functions from arnie). My code probably needs to be changed to incorporate the same functionality.
Testing
I had manually tested and ensured that batched (fast) and unbatched (slow) score functions give the exact same outputs for large amounts of RNAs.
Automated testing has not been implemented, but perhaps it would be good to have unit tests.
Related Issues
NA