Repository navigation
Hackathon retreat 2026 - #404
Merged
Merged
Conversation
…ures/ptm_pipeline
- Introduced `run_generate_training_data` function to manage training data generation. - Updated `run_job` to include a case for "GenerateTrainingData". - Modified `Config` class to include `run_original` attribute for better state management. - Adjusted job type documentation to reflect new functionality.
…export function to use original tab filenames
Feature/generate training data
…nergy handling in _get_best_ce function for better calibration results.
…_ENERGY, and PRECURSOR_CHARGE; streamline hcd_targets processing
…able GPU when no GPUs available.
…ng with parallelization
Feature/dlomix integration
…ibration doctest Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…tures/dia-support
DIA support
- add `acquisitionMethod` config option ("DDA" default, or "DIA") and document it
- build DIA spectral library rows (parallelized), including gene names
extracted from protein identifiers
- CE calibration for DIA calibrates one CE per precursor charge
CE calibration
- DDA calibrates one CE per original CE instead of a single global CE;
RANSAC still applies a per-spectrum offset to each spectrum's own CE
- alignment keeps only the best-scoring PSM per RAW_FILE/SCAN_NUMBER
- only HCD spectra are calibrated; non-HCD spectra (e.g. CID) are set to 35
- fix KeyError in DDA without RANSAC (ORIG_COLLISION_ENERGY only exists in
the alignment library)
- assign calibrated CEs in one step so an already assigned CE is not
remapped by another group; uncalibrated HCD groups keep their original CE
- write calibration plots and per-group results to results/ce_calibration
Rescoring
- merge_input fills NaNs per tab file, optionally in parallel (num_threads)
- percolator uses config.num_threads
- ExpMass is now computed by spectrum_fundamentals' Percolator; depend on
spectrum-fundamentals from the development branch until it is released
Tests
- add CE calibration tests for DDA, DDA with RANSAC, DIA and CID-only data
- update expected rescoring test data for the ExpMass column
- fix ce_calibration doctest (SCAN_NUMBER now required)
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## development #404 +/- ##
================================================
- Coverage 60.16% 49.98% -10.19%
================================================
Files 24 26 +2
Lines 2164 3251 +1087
Branches 282 471 +189
================================================
+ Hits 1302 1625 +323
- Misses 754 1545 +791
+ Partials 108 81 -27
Flags with carried forward coverage won't be shown. Click here to find out more.
🚀 New features to boost your workflow:
|
- fix DIA spectral library export (missing ExpMass, charge parsing, dedup) - document GenerateTrainingData, web UI, new outputs and python requirements - add 1.0.0 news entry with breaking changes - add tests for DLOmix predictor, DIA spectral library and training data job
…ured - fall back to HCD with a warning for unknown, unsupported or mixed methods - only calibrate CE for spectra labelled HCD, matching the alignment selection
…tures/ptm_pipeline
…rfest into features/ptm_pipeline
Features/ptm pipeline
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
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.
No description provided.