Improve runtime for predict_library by running DeepLC and IM2Deep predictions only once #243
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
1 participant
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Outdated suggestions cannot be applied.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.
Key changes:
Changes to
predict_libraryfunction:PSMListand filtering of PSMs by mz inpredict_libraryfunction (ms2pip/core.py).ms2pip/core.py).Improvements in
search_spacehandling:to_psm_listmethod to convert search space toPSMList(ms2pip/search_space.py).buildmethod to ensure the number of processes is correctly set and used for parallelization (ms2pip/search_space.py).Timing of runs on
releasesand this branch, on a small fasta subset of human proteome (semi-tryptic) (~240.000 PSMs, so 3 batches):releases: 3099.83s user 1460.12s system 1312% cpu 5:47.51 totalthis branch: 2405.46s user 596.67s system 1334% cpu 3:44.90 total