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Recent Releases of https://github.com/compomics/ms2rescore

https://github.com/compomics/ms2rescore - v3.1.5

Fixed

  • 🐛 Fixed compatibility with Numpy 2: Usage of np.inf instead of `np.Inf (PR #224, fixes #219)

- Python
Published by RalfG 10 months ago

https://github.com/compomics/ms2rescore - v3.2.0.dev2

What's Changed

  • Fix silent crash due to XGBoost-CUDA environment variable incompatibility by @RalfG in https://github.com/compomics/ms2rescore/pull/216
  • Update pyproject.toml, version bump IM2Deep by @rodvrees in https://github.com/compomics/ms2rescore/pull/214
  • Add IM2Deep to citations GUI by @rodvrees in https://github.com/compomics/ms2rescore/pull/215
  • CI: Update action versions by @RalfG in https://github.com/compomics/ms2rescore/pull/217

Full Changelog: https://github.com/compomics/ms2rescore/compare/3.2.0.dev1...v3.2.0.dev2

- Python
Published by RalfG 11 months ago

https://github.com/compomics/ms2rescore - 3.2.0.dev1

What's Changed

  • Switch to FlashLFQ output from psm_utils by @RalfG in https://github.com/compomics/ms2rescore/pull/186
  • Support gzipped spectra files (and Thermo raw!) by @paretje in https://github.com/compomics/ms2rescore/pull/184
  • Refactor parsing of precursor data from spectrum files by @RalfG in https://github.com/compomics/ms2rescore/pull/162

Still planned for 3.2.0, but not yet included

  • Spectrum feature generator and Mumble integration (#178)

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.4...3.2.0.dev1

- Python
Published by RalfG about 1 year ago

https://github.com/compomics/ms2rescore - v3.1.4

Fixed

  • Update im2deep import after API change in v0.3.1 (#205, fixes #204, by @ArthurDeclercq)

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.3...v3.1.4

- Python
Published by RalfG about 1 year ago

https://github.com/compomics/ms2rescore - v3.1.3

Fixed

  • 📌 Pin DeepLC version to <3.1, avoiding calibration bug by @RalfG in https://github.com/compomics/ms2rescore/pull/198
  • 📌 Pin pyOpenMS (upstream dependency for psm_utils) (see openMS/openMS#7600) by @RalfG in https://github.com/compomics/ms2rescore/pull/199
  • 📝 Fix incorrect decoy pattern configuration in documentation example by @rodvrees in https://github.com/compomics/ms2rescore/pull/191
  • 🐛 Fix UnicodeEncodeError when running IM2Deep (similar to DeepLC issue #188) @ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/195

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.2...v3.1.3

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.2

Changed

  • 🚸 GUI: Improve user experience with descriptions, open report upon finishing, etc. (#175)
  • ⬆️ Update dependency versions; drop support for Python 3.8 (required for TensorFlow versions; EOL soon) (#189)

Fixed

  • 🚨 Fix ruff linting for tutorial notebook (was not checked by previous versions of Ruff) (#180)
  • 📝 Minor documentation updates: Update overview figure; refer to ms2rescore.rescore in Python API tutorial; remove v3.0 warning in readme (#181)
  • 📝 Fix README URLs to documentation pages (#187)
  • 🐛 Fix bug where the default TIMS²Rescore configuration items always overwrote user configuration (#176)
  • 🐛 Fix non-descriptive IndexError in Qvality when PEP cannot be calculated (see statisticalbiotechnology/triqler#29). To be updated when addressed upstream. (#182, fixes #165)
  • 🐛 Fix UnicodeEncodeError when running DeepLC with transfer learning (#188, fixes #183 and #185)

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.1

Fixed

  • 👷 CI: Add missing ionmob dependency for Windows installer by @RalfG in https://github.com/compomics/ms2rescore/pull/163 and https://github.com/compomics/ms2rescore/pull/173
  • 🐛 GUI: Correctly parse IM2Deep config in GUI (fixes #172) by @ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/172
  • 🐛 Limit Percolator processes to 128 (fixes #117) by @RalfG in https://github.com/compomics/ms2rescore/pull/169

Deployment

  • 🚀 From this release onward, Docker images will be build and pushed to GHCR (by @paretje in https://github.com/compomics/ms2rescore/pull/167)

New Contributors

  • @paretje made their first contribution in https://github.com/compomics/ms2rescore/pull/167

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.2...v3.1.1

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.0

Added

  • ✨ New tims2rescore CLI entrypoint with TIMS-specific configuration defaults
  • ✨ IM2Deep feature generator for ion mobility
  • ✨ Support for Bruker raw (.d) and miniTDF formats (was also back-ported to v3.0.3)
  • ✨ psm_id_rt_pattern and psm_id_im_pattern: New options to allow parsing of RT/IM from PSM file spectrum identifiers.
  • ✨ max_psm_rank_input and max_psm_rank_output: New options to control rescoring and reporting of multiple PSMs per spectrum (default 5 and 1)
  • ✨ Also store peptide-level q-value and PEPs in the output PSM list, under the metadata field.
  • ✨ profile option to write a cProfile report of the rescoring process (for debugging)
  • ✨ Option to pass train_fdr to Mokapot (test_fdr was already supported as kwarg)
  • ⚡ Faster spectrum file reading with timsrust and mzdata Rust libraries
  • 📝 Add TIMS²Rescore docs and citation on README; more detailed docs on formula modifications

Changed

  • 👷 CI: Lint with ruff instead of flake8
  • ⚡ DeepLC: By default use PSMs initially passing 1% FDR threshold for calibration instead of a fixed number
  • 🔊 DeepLC: Throw warning when using deeplc_retrain with less than 500 calibration PSMs
  • 🔊 Raise exception if missing precursor info (retention time or ion mobility) could not found in both PSM and spectrum files.
  • ⬆️ Update (and sort) dependencies in pyproject.toml
  • 📦 Dockerfile: Use Python 3.11 base image instead of Ubuntu
  • 🔧 Config: Change write_report default value from true to false

Fixed

  • 🐛 Report: Fix calculation of number of retained peptides in identification overlap chart
  • 🐛 DeepLC: Fix issue with conversion to PEPREC (fixes #108, fixes #113)
  • 🐛 Fix bug in inferspectrumpath if path in configuration is None
  • 🐛 Fix bug that always set im_required to True, even if no IM-based feature generators were configured.

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.3...v3.1.0

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.0-dev9

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev8...v3.1.0-dev9

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.0-dev9

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev8...v3.1.0-dev9

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.0-dev8

Full Changelog: https://github.com/compomics/ms2rescore/compare/3.1.0-dev7...v3.1.0-dev8

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - 3.1.0-dev7

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev6...3.1.0-dev7

- Python
Published by RalfG over 1 year ago

https://github.com/compomics/ms2rescore - v3.1.0-dev6

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev5...v3.1.0-dev6

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.1.0-dev5

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev4...v3.1.0-dev5

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.1.0-dev4

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev3...v3.1.0-dev4

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.1.0-dev3

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev2...v3.1.0-dev3

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.1.0-dev2

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.1.0-dev1...v3.1.0-dev2

- Python
Published by ArthurDeclercq almost 2 years ago

https://github.com/compomics/ms2rescore - v3.1.0-dev1

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.3...v3.1.0-dev1

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.0.3

Added

  • Allow user to pass model_dir to MS²PIP in feature generator (fixes #134)

Changed

  • Missing precursor information (retention time and ion mobility) is now parsed in Rust using mzdata and timsrust, adding the new ms2rescore-rs package. This change also adds support for Bruker TDF and miniTDF raw files for this feature.
  • Use single quotes instead of back ticks when logging strings for improved Rich formatting.
  • Reactivate tests in CI.

Fixed

  • Fix writing of FlashLFQ output file with Mokapot when PSM List run fields are empty.
  • Write partial report when confidence before could not be calculated (e.g., when no PSMs identified before rescoring)

Windows installer Includes changes from upstream tools:

  • psmutils: https://github.com/compomics/psmutils/compare/v0.7.3...v0.8.2
  • MS²PIP: https://github.com/compomics/ms2pip/compare/v4.0.0-dev8...v4.0.0-dev10

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.2...v3.0.3

- Python
Published by RalfG almost 2 years ago

https://github.com/compomics/ms2rescore - v3.0.2

Fixed

  • Remove PSMs with invalid amino acids to avoid errors in feature generators (#126 )

- Python
Published by ArthurDeclercq almost 2 years ago

https://github.com/compomics/ms2rescore - v3.0.1

Fixed

  • Don't use unsupported icon on Linux systems (fixes #118)

Changed

  • Improved exception handling and logging for report generation
  • Update deeplc_retrainer version
  • Pin Numpy version for Python 3.11 (incompatibility between pyGAM, sklearn, and tensorflow)

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0...v3.0.1

- Python
Published by RalfG about 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0

New in MS²Rescore v3 🎉

  • Use of psm_utils to support over 10 PSM file formats from different search engines
  • Support for mzML (MGF still supported)
  • HTML output with interactive charts for quality control and result inspection
  • High modularity in Python package to faciliate implementation in other workflows
  • Documentation on https://ms2rescore.readthedocs.io
  • ionmob feature generator for ion mobility CCS predictions
  • mokapot rescoring engine for more efficient rescoring
  • New graphical user interface with one-click installer for Windows
  • Many minor improvements (read more in our preprint: https://doi.org/10.26434/chemrxiv-2023-rvr9n)

Full Changelog: https://github.com/compomics/ms2rescore/compare/v2.1.3...v3.0.0

- Python
Published by RalfG about 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-b5

What's Changed

  • Fix build of Windows PyInstaller by @RalfG in https://github.com/compomics/ms2rescore/pull/102
  • Better logging for modification mapping; fix pyOpenMS issue in Dockerfile by @ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/103

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0b4...v3.0.0-b5

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0b4

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0-b3...v3.0.0b4

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-b3

Full Changelog: https://github.com/compomics/ms2rescore/compare/3.0.0b2...v3.0.0-b3

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - 3.0.0b2

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0-b1...3.0.0b2

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-b1

What's Changed

  • v3 by @RalfG in https://github.com/compomics/ms2rescore/pull/84
  • Add ionmob feature generator by @RalfG in https://github.com/compomics/ms2rescore/pull/95
  • Add and update examples (move data to external site, add config files) by @RalfG in https://github.com/compomics/ms2rescore/pull/96
  • Multiple id input files by @ArthurDeclercq in https://github.com/compomics/ms2rescore/pull/97

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0-dev4...v3.0.0-b1

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-dev4

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0-dev3...v3.0.0-dev4

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-dev3

Full Changelog: https://github.com/compomics/ms2rescore/compare/v3.0.0-dev2...v3.0.0-dev3

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-dev2

Early development release of v3

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v3.0.0-dev1

Early development release of v3

- Python
Published by RalfG over 2 years ago

https://github.com/compomics/ms2rescore - v2.1.3

Bugfixes 🪲

  • GUI: Fixed parsing of new-style MaxQuant modification names (#76, backport of #75)

- Python
Published by RalfG over 3 years ago

https://github.com/compomics/ms2rescore - v2.1.2

Improvements 🚀

  • Additional PEAKS search engine features

Bugfixes 🪲

  • Changed peptideshaker name in the
  • Fix the mgf title field extraction to be compatible with PEAKS XPro output (fixes #44)
  • Removed shell=True option from Percolator command (fixes #55)
  • MS²Rescore now returns an error if an error occured while running Percolator (added check=True to subprocess.run)
  • Deprecation warning "passing set as indexer" fix
  • Python 3.9 compatibility for GUI

Refactoring and minor changes 🔧

  • Ignore Deprecation-/Future-/UserWarnings in GUI mode (fixes https://github.com/compomics/ms2rescore/issues/61)
  • Cleanup imports and remove importlib_resources backport (Python 3.6 compatibility not needed anymore)
  • Set Gooey target to allow gui startup from ms2rescore-gui entrypoint and add ms2rescore-gui entrypoint (GUI can now be started from the terminal with both python -m ms2rescore.gui and ms2rescore-gui).
  • Relax scikit-learn dependency to <2 (v1.0.0 now released)
  • Fix UserWarning in percolator.py (unused groups in regex for Pandas str.match())

- Python
Published by ArthurDeclercq almost 4 years ago

https://github.com/compomics/ms2rescore - v2.1.1

Improvements 🚀

  • Refactored parsing of MaxQuant Modified sequence to allow for new long form modification labels (e.g. PEPM(Oxidation (M)K instead of PEPM(ox)K) (PR #47, fixes #41)
  • Added regex pattern option to the config to allow more flexible PSM ID matching with the MGF TITLE field (PR #42)
  • Added MGF TITLE pattern, num CPU, and feature set options to the GUI (PR #43)

Bugfixes 🪲

  • Spaces and hyphens are now supported for input file names (Changed Percolator subprocess command) (PR #43)
  • Set default value of mgf_title_pattern to None to be compatible with PEAKS pipeline (PR #46)

Refactoring and minor changes 🔧

  • Removed print statement from idfileparser module (PR #42)
  • Replaced deprecated pandas functions (PR #46)

- Python
Published by RalfG almost 4 years ago

https://github.com/compomics/ms2rescore - v2.1.0

Improvements 🚀

  • Added support for PEAKS mzid identification files!
  • Retention time predictor calibrates now for each raw file independently resulting in more accurate calibrations.

Bugfixes 🪲

  • MaxQuant pipeline: Carbamidomethyl is not listed as default fixed modification anymore, as this could not be overridden. Searches without carbamidomethyl as fixed modification are now supported. However, carbamidomethyl now always needs to be specified explicitly if applicable!
  • When parsing MGF files, all lines ending on 0.0 (including lines ending on 10.0) were removed, instead of only 0 intensity peaks. This is now fixed.

Refactoring and minor changes 🔧

  • PIN pipeline: Allow mass shift modification labels with + sign (e.g. R.IM[+15.99492]MAR.D).
  • PEAKS and MaxQuant pipelines: Precursor charge from ID file now overwrites CHARGE in MGF file. (Identification and instrument precursor charges do not always match; identification charge should be prioritized).
  • Plotting module can only be run when Percolator is run as part of MS²Rescore.
  • If no decoy PSMs are present, MS²Rescore raises an error and stops.
  • Removed obsolete mgf option from maxquant_to_rescore configuration.

PR #35

- Python
Published by RalfG about 4 years ago

https://github.com/compomics/ms2rescore - v2.0.0

Improvements 🚀

  • MS²Rescore now runs on Windows!
  • Graphical user interface (GUI) added, built with Gooey Install with pip install ms2rescore[gui] and run python -m ms2rescore.gui
  • Install, upgrade, and run scripts added for Windows users without an existing Python installation who simply want to use the new GUI
  • MS²Rescore can now output a PDF with useful plots displaying the results.

Refactoring and minor changes 🔧

  • ⚠️Breaking change: MS²Rescore is now written with a lowercase S (instead of "MS²ReScore). This means that some class names and exceptions have been renamed accordingly, breaking the Python API with previous versions.
  • ⚠️Breaking change: The feature_sets option now expects instead of a string with a predefined feature set, such as ms2pip_rt, a list of strings including one of the following: searchengine, rt, or ms2pip. By default, MS²Rescore uses all features: ['searchengine', 'rt', 'ms2pip'].
  • MS²PIP is now imported and called through the Python API instead of the CLI

Includes PRs #34 and #37.

- Python
Published by RalfG over 4 years ago

https://github.com/compomics/ms2rescore - v2.0.0-beta.5

Improvements 🚀

  • PSMs with invalid amino acids (B, J, O, U, X, and Z), which are unsupported by MS²PIP, are now removed in all pipelines (Fixes #31).

Bugfixes 🐛

  • Case-insensitive matching of msms.txt column names (e.g. both Mass Deviations [Da] and Mass deviations [Da] will now both be accepted)
  • Fix MGF title parsing in MaxQuant pipeline

Refactoring and minor changes 🔧

  • Replaced assertions with specific exceptions
  • Removed empty module runner.py
  • Dropped support for Python 3.6 (did not work with subprocess capture_output)

- Python
Published by RalfG almost 5 years ago

https://github.com/compomics/ms2rescore - v2.0.0-beta.4

Fixed:

  • Prevent duplicate columns in pin output

- Python
Published by RalfG about 5 years ago

https://github.com/compomics/ms2rescore - v2.0.0-beta.3

New: - X!Tandem pipeline outputs flanking amino acids to PIN file (#24, #27)

Fixed: - Temporary fix for Tensorflow NUMEXPRMAXTHREADS (#25, compomics/DeepLC#19) - tandem_id column was erroneously written to X!Tandem PIN files - Use logger instead of logging

- Python
Published by RalfG about 5 years ago

https://github.com/compomics/ms2rescore - v2.0.0-beta.2

New and fixed: - Rescore with DeepLC retention time prediction - New pipeline for X!Tandem search results - Support for C-terminal modifications - Simplified configuration (see README.md and configuration.md) - By default, the pipeline is inferred from the identification file extension - Major code refactoring - Many bugfixes - Installable from PyPI

- Python
Published by RalfG about 5 years ago

https://github.com/compomics/ms2rescore - v0.2.2

Before DeepLC integration and refactoring.

- Python
Published by RalfG over 5 years ago