Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

TIMS²Rescore #142

Merged
merged 129 commits into from
Jul 17, 2024
Merged

TIMS²Rescore #142

merged 129 commits into from
Jul 17, 2024

Conversation

RalfG
Copy link
Member

@RalfG RalfG commented Apr 8, 2024 •
edited
Loading

Added

  • ✨ New tims2rescore CLI entrypoint with TIMS-specific configuration defaults
  • ✨ IM2Deep feature generator for ion mobility
  • ✨ Support for Bruker raw (.d) and miniTDF formats
  • ✨ 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.

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

Fixed

ArthurDeclercq and others added 30 commits November 22, 2023 14:04
@ArthurDeclercq
parsing from spectrum id
50aff5e
@ArthurDeclercq
change regex function used
dcfcc00
@ArthurDeclercq
fix unboundLocalError
25aa0ea
@ArthurDeclercq
add regex patterns for im and rt parsing from spectrum id
0e2b192
@rodvrees
im2deep
b45007f
@ArthurDeclercq
add debug statement for im, rt parsing
112860c
@rodvrees
Merge remote-tracking branch 'origin/timsRescore' into timsRescore
0330096
@rodvrees
models + debug
f6c9564
@rodvrees
fix
7585d51
@rodvrees
add models
a0f792f
@rodvrees
fixes in im2deep.py
b4660fd
@rodvrees
fixes in im2deep.py
1a18a42
@rodvrees
im2deep implementation
b93df98
@ArthurDeclercq
remove peprec implementation deeplc
8749ddf
@rodvrees
CCS shift calculation fix
782c7a0
@rodvrees
models + plot
7604153
@ArthurDeclercq
add inverse reduced ion mobility key to mzml parsing
b2d65eb
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
aa9cde0
@ArthurDeclercq
remove print statements
230753c
@ArthurDeclercq
updated inverse reduced ion mobility
d9f9feb
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
6ccb429
@ArthurDeclercq
add unused argument
00d6704
@ArthurDeclercq
skip ms1 scans in mzml
50a01e9
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
2645378
@rodvrees
IM2Deep plot correct labels
a99b492
@rodvrees
calibrate per charge option
1f6e973
@rodvrees
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
301d632 
…sRescore
@rodvrees
new models and reference
dd8bd18
@rodvrees
correct format reference
ad0f3d7
@rodvrees
fix model name in IM2Deep
3a5b1ab
RalfG and others added 11 commits April 18, 2024 10:45
@RalfG
Mokapot: Fix merging peptide level info if run is None
dcb5515
@RalfG
Report: Move some loggings from info to debug
9a0514e
@RalfG
Version bump
9409d68
@ArthurDeclercq
peptide level bug fix
5d804ea
@RalfG
Version bump
37ba9db
@RalfG
Upgrade to psm_utils v0.9, which now uses Pydantic v2
2a947ee
@RalfG
Added:
3047f28 
- Add option to pass train_fdr to mokapot;

Changed:
- Split functions to add mokapot confidence
- Implement workaround for broken PEP calculation if best PSM is decoy
- Still write PSMs to file, even if rescoring step failed. Still skip report generation
@RalfG
Split removing invalid AAs from reading PSM files step. Now also work…
02f775b 
…s when passed an in-memory PSMList.
@RalfG
Upgrade to Pyteomics 4.7.2 (contains caching of resolved modifications)
54f0fe5
@RalfG
Relax numpy version requirement
d483615
@RalfG
Explicitly add scikit-learn 1.5.1 to dependencies
6b46fda
RalfG and others added 5 commits July 4, 2024 19:29
@RalfG
Version bump
a0b9ce4
@RalfG
Add options max_psm_rank_input and max_psm_rank_output to control…
bc6c314 
… multi-rank rescoring.
@RalfG
Version bump
1f0915c
@paretje
only install binary distributions
7744391 
I'm not sure why during the resolve, pip tries sckit-learn 1.1.2, and
that requires a build, which fails. The same thing happens using `pip
install --ignore-installed --dry-run .`. But generally, it probably
makes sense to avoid compiling from source in a github action.
@RalfG
Explicitly pass scores to 'assign_confidence' to avoid 'no psms under…
e3f723d 
… eval_fdr' error when calculating q-values and PEPs.
@RalfG RalfG marked this pull request as ready for review July 9, 2024 11:15
@RalfG RalfG requested a review from paretje July 9, 2024 11:15
@RalfG RalfG mentioned this pull request Jul 17, 2024
Closed
@ArthurDeclercq ArthurDeclercq merged commit df3ceda into main Jul 17, 2024
5 checks passed
@ArthurDeclercq ArthurDeclercq deleted the timsRescore branch July 17, 2024 11:20
@RalfG RalfG restored the timsRescore branch July 18, 2024 13:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@paretje paretje Awaiting requested review from paretje

Assignees
No one assigned
Labels
enhancement
Projects
None yet
Milestone
v3.1.0
4 participants
@RalfG @ArthurDeclercq @rodvrees @paretje