ms2rescore 3.2.0.dev2__tar.gz → 3.2.0.post1__tar.gz

ms2rescore-3.2.0.post1/PKG-INFO

@@ -0,0 +1,358 @@
+Metadata-Version: 2.3
+Name: ms2rescore
+Version: 3.2.0.post1
+Summary:  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications.
+Keywords: MS2Rescore,MS2PIP,DeepLC,Percolator,proteomics,mass spectrometry,peptide identification,rescoring,machine learning
+Author: Ralf Gabriels, Arthur Declercq, Ana Sílvia C. Silva, Robbin Bouwmeester, Louise Buur
+Author-email: Ralf Gabriels <ralf@gabriels.dev>, Arthur Declercq <arthur.declercq@ugent.be>
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+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Development Status :: 5 - Production/Stable
+Requires-Dist: cascade-config>=0.4.0
+Requires-Dist: click>=7
+Requires-Dist: customtkinter>=5,<6
+Requires-Dist: deeplc>=3.1
+Requires-Dist: deeplcretrainer
+Requires-Dist: im2deep>=0.3.1
+Requires-Dist: jinja2>=3
+Requires-Dist: lxml>=4.5
+Requires-Dist: mokapot==0.10
+Requires-Dist: ms2pip>=4.0.0
+Requires-Dist: ms2rescore-rs>=0.4.3
+Requires-Dist: numpy>=1.25
+Requires-Dist: packaging>=25.0
+Requires-Dist: pandas>=1
+Requires-Dist: plotly>=5
+Requires-Dist: psm-utils>=1.1
+Requires-Dist: pyteomics>=4.7.2
+Requires-Dist: rich>=12
+Requires-Dist: tomli>=2 ; python_full_version < '3.11'
+Requires-Dist: pyopenms>=3.3 ; extra == 'idxml'
+Requires-Dist: ionmob>=0.2 ; extra == 'ionmob'
+Requires-Dist: tensorflow ; extra == 'ionmob'
+Requires-Python: >=3.10
+Project-URL: CompOmics, https://www.compomics.com
+Project-URL: GitHub, https://github.com/compomics/ms2rescore
+Project-URL: PyPi, https://pypi.org/project/ms2rescore/
+Project-URL: ReadTheDocs, https://ms2rescore.readthedocs.io
+Provides-Extra: idxml
+Provides-Extra: ionmob
+Description-Content-Type: text/markdown
+
+<img src="https://github.com/compomics/ms2rescore/raw/main/img/ms2rescore_logo.png" width="150" height="150" alt="MS²Rescore"/>
+<br/><br/>
+
+[![GitHub release](https://img.shields.io/github/release-pre/compomics/ms2rescore.svg?style=flat-square)](https://github.com/compomics/ms2rescore/releases)
+[![PyPI](https://flat.badgen.net/pypi/v/ms2rescore)](https://pypi.org/project/ms2rescore/)
+[![GitHub Workflow Status](https://flat.badgen.net/github/checks/compomics/ms2rescore/main)](https://github.com/compomics/ms2rescore/actions/)
+[![GitHub issues](https://img.shields.io/github/issues/compomics/ms2rescore?style=flat-square)](https://github.com/compomics/ms2rescore/issues)
+[![GitHub](https://img.shields.io/github/license/compomics/ms2rescore.svg?style=flat-square)](https://www.apache.org/licenses/LICENSE-2.0)
+[![Last commit](https://flat.badgen.net/github/last-commit/compomics/ms2rescore)](https://github.com/compomics/ms2rescore/commits/)
+
+Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
+
+## About MS²Rescore
+
+MS²Rescore performs ultra-sensitive peptide identification rescoring with LC-MS predictors such as
+[MS²PIP][ms2pip] and [DeepLC][deeplc], and with ML-driven rescoring engines
+[Percolator][percolator] or [Mokapot][mokapot]. This results in more confident peptide
+identifications, which allows you to get **more peptide IDs** at the same false discovery rate
+(FDR) threshold, or to set a **more stringent FDR threshold** while still retaining a similar
+number of peptide IDs. MS²Rescore is **ideal for challenging proteomics identification workflows**,
+such as proteogenomics, metaproteomics, or immunopeptidomics.
+
+![MS²Rescore overview](https://raw.githubusercontent.com/compomics/ms2rescore/main/docs/source/_static/img/ms2rescore-overview.png)
+
+MS²Rescore can read peptide identifications in any format supported by [psm_utils][psm_utils]
+(see [Supported file formats][file-formats]) and has been tested with various search engines output
+files:
+
+- [MS Amanda](http://ms.imp.ac.at/?goto=msamanda) `.csv`
+- [Sage](https://github.com/lazear/sage) `.sage.tsv`
+- [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) `.mzid`
+- [ProteomeDiscoverer](#)`.msf`
+- [MSGFPlus](https://omics.pnl.gov/software/ms-gf) `.mzid`
+- [Mascot](https://www.matrixscience.com/) `.mzid`
+- [MaxQuant](https://www.maxquant.org/) `msms.txt`
+- [X!Tandem](https://www.thegpm.org/tandem/) `.xml`
+- [PEAKS](https://www.bioinfor.com/peaksdb/) `.mzid`
+
+MS²Rescore is available as a [desktop application][desktop], a [command line tool][cli], and a
+[modular Python API][python-package].
+
+## TIMS²Rescore: Direct support for DDA-PASEF data
+
+MS²Rescore v3.1+ includes TIMS²Rescore, a usage mode with specialized default configurations for
+DDA-PASEF data from timsTOF instruments. TIMS²Rescore makes use of new MS²PIP prediction models for
+timsTOF fragmentation and IM2Deep for ion mobility separation. Bruker .d and miniTDF spectrum
+files are directly supported through the [timsrust](https://github.com/MannLabs/timsrust) library.
+
+Checkout our [paper](https://doi.org/10.1021/acs.jproteome.4c00609) for more information and the
+[TIMS²Rescore documentation][tims2rescore] to get started.
+
+## Citing
+
+**Latest MS²Rescore publication:**
+
+> **MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0.**
+> Louise Marie Buur*, Arthur Declercq*, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer*, and Ralf Gabriels*.
+> _Journal of Proteome Research_ (2024) [doi:10.1021/acs.jproteome.3c00785](https://doi.org/10.1021/acs.jproteome.3c00785) <br/> \*contributed equally <span class="__dimensions_badge_embed__" data-doi="10.1021/acs.jproteome.3c00785" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+
+**MS²Rescore for immunopeptidomics:**
+
+> **MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates.**
+> Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, and Ralf Gabriels.
+> _Molecular & Cellular Proteomics_ (2021) [doi:10.1016/j.mcpro.2022.100266](https://doi.org/10.1016/j.mcpro.2022.100266) <span class="__dimensions_badge_embed__" data-doi="10.1016/j.mcpro.2022.100266" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+
+**MS²Rescore for timsTOF DDA-PASEF data:**
+
+> **TIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore.**
+> Arthur Declercq*, Robbe Devreese*, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R Krieger, Tharan Srikumar, George Rosenberger, Dennis Trede, Christine Carapito, Stefan Tenzer, Juliane S Walz, Sven Degroeve, Robbin Bouwmeester, Lennart Martens, and Ralf Gabriels.
+> _Journal of Proteome Research_ (2025) [doi:10.1021/acs.jproteome.4c00609](https://doi.org/10.1021/acs.jproteome.4c00609) <span class="__dimensions_badge_embed__" data-doi="10.1021/acs.jproteome.4c00609" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+
+**Original publication describing the concept of rescoring with predicted spectra:**
+
+> **Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions.**
+> Ana S C Silva, Robbin Bouwmeester, Lennart Martens, and Sven Degroeve.
+> _Bioinformatics_ (2019) [doi:10.1093/bioinformatics/btz383](https://doi.org/10.1093/bioinformatics/btz383) <span class="__dimensions_badge_embed__" data-doi="10.1093/bioinformatics/btz383" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+
+To replicate the experiments described in this article, check out the
+[publication branch][publication-branch] of the repository.
+
+## Getting started
+
+The desktop application can be installed on Windows with a [one-click installer][desktop-installer].
+The Python package and command line interface can be installed with `pip`, `conda`, or `docker`.
+Check out the [full documentation][docs] to get started.
+
+## Questions or issues?
+
+Have questions on how to apply MS²Rescore on your data? Or ran into issues while using MS²Rescore?
+Post your questions on the [GitHub Discussions][discussions] forum and we are happy to help!
+
+## How to contribute
+
+Bugs, questions or suggestions? Feel free to post an issue in the [issue tracker][issues] or to
+make a [pull request][pr]!
+
+[docs]: https://ms2rescore.readthedocs.io/
+[issues]: https://github.com/compomics/ms2rescore/issues/
+[discussions]: https://github.com/compomics/ms2rescore/discussions/
+[pr]: https://github.com/compomics/ms2rescore/pulls/
+[desktop]: https://ms2rescore.readthedocs.io/en/stable/gui/
+[desktop-installer]: https://github.com/compomics/ms2rescore/releases/latest
+[cli]: https://ms2rescore.readthedocs.io/en/stable/cli/
+[python-package]: https://ms2rescore.readthedocs.io/en/stable/api/ms2rescore/
+[docker]: https://ms2rescore.readthedocs.io/en/stable/installation#docker-container
+[publication-branch]: https://github.com/compomics/ms2rescore/tree/pub
+[ms2pip]: https://github.com/compomics/ms2pip
+[deeplc]: https://github.com/compomics/deeplc
+[percolator]: https://github.com/percolator/percolator/
+[mokapot]: https://mokapot.readthedocs.io/
+[psm_utils]: https://github.com/compomics/psm_utils
+[file-formats]: https://psm-utils.readthedocs.io/en/stable/#supported-file-formats
+[tims2rescore]: https://ms2rescore.readthedocs.io/en/stable/userguide/tims2Rescore

ms2rescore-3.2.0.post1/ms2rescore/__init__.py

@@ -0,0 +1,34 @@
+"""Modular and user-friendly platform for AI-assisted rescoring of peptide identifications ."""
+
+# __version__ is provided by the small helper module _version which prefers
+# installed distribution metadata and falls back to reading pyproject.toml.
+# The single source of truth for the version is pyproject.toml.
+
+__all__ = [
+    "parse_configurations",
+    "rescore",
+]
+
+from warnings import filterwarnings
+
+# mzmlb is not used, so hdf5plugin is not needed
+filterwarnings(
+    "ignore",
+    message="hdf5plugin is missing",
+    category=UserWarning,
+    module="psims.mzmlb",
+)
+
+# Attempt to suppress pyopenms warning about OPENMS_DATA_PATH already set
+filterwarnings(
+    "ignore",
+    message="Warning: OPENMS_DATA_PATH environment variable already exists.*",
+    category=UserWarning,
+    module="pyopenms",
+)
+
+from ms2rescore._version import get_version  # noqa: E402
+from ms2rescore.config_parser import parse_configurations  # noqa: E402
+from ms2rescore.core import rescore  # noqa: E402
+
+__version__ = get_version()

{ms2rescore-3.2.0.dev2 → ms2rescore-3.2.0.post1}/ms2rescore/__main__.py

@@ -14,6 +14,7 @@ from rich.logging import RichHandler
 from rich.text import Text
 
 from ms2rescore import __version__, package_data
+from ms2rescore._version import check_for_update
 from ms2rescore.config_parser import parse_configurations
 from ms2rescore.core import rescore
 from ms2rescore.exceptions import MS2RescoreConfigurationError
@@ -148,18 +149,24 @@ def _argument_parser() -> argparse.ArgumentParser:
     )
     parser.add_argument(
         "--write-report",
-        # metavar="BOOL",
         action="store_true",
+        default=None,
         dest="write_report",
-        help="boolean to enable profiling with cProfile",
+        help="boolean whether to write an HTML report (default: True)",
+    )
+    parser.add_argument(
+        "--disable-update-check",
+        action="store_true",
+        default=None,
+        dest="disable_update_check",
+        help="Disable automatic check for software updates (default: False)",
     )
     parser.add_argument(
         "--profile",
-        # metavar="BOOL",
         action="store_true",
-        # type=bool,
-        # dest="profile",
-        help="boolean to enable profiling with cProfile",
+        default=None,
+        dest="profile",
+        help="Enable profiling with cProfile",
     )
 
     return parser
@@ -228,9 +235,19 @@ def main(tims=False):
         config["ms2rescore"]["log_level"], config["ms2rescore"]["output_path"] + ".log.txt"
     )
 
+    # Check for updates
+    if config["ms2rescore"]["disable_update_check"] is False:
+        update_info = check_for_update()
+        if update_info["update_available"]:
+            LOGGER.info(
+                f"New version of MS²Rescore available: {update_info['latest_version']} "
+                f"(you are using {update_info['current_version']})"
+            )
+            LOGGER.info(f"Download the latest version at: {update_info['html_url']}")
+
     # Run MS²Rescore
     try:
-        if cli_args.profile:
+        if config["ms2rescore"]["profile"]:
             profiled_rescore = profile(rescore, config["ms2rescore"]["output_path"])
             profiled_rescore(configuration=config)
         else:

ms2rescore-3.2.0.post1/ms2rescore/_version.py

@@ -0,0 +1,135 @@
+"""
+Resolve the package version.
+
+Prefer installed distribution metadata (importlib.metadata); if the package is not installed, fall
+back to reading ``pyproject.toml`` from the repository root (PEP 621: ``[project].version``).
+"""
+
+import importlib.metadata
+import json
+import logging
+from pathlib import Path
+from typing import Dict, Optional, Tuple, Union
+from urllib.error import HTTPError, URLError
+from urllib.request import Request, urlopen
+
+from packaging.version import Version
+
+try:
+    import tomllib as toml  # type: ignore
+except ImportError:
+    import tomli as toml  # type: ignore
+
+from ms2rescore.exceptions import MS2RescoreError
+
+LOGGER = logging.getLogger(__name__)
+
+_GITHUB_REPO = "CompOmics/ms2rescore"
+_GITHUB_TIMEOUT_SECONDS = 2.5
+
+
+class UpdateCheckError(MS2RescoreError):
+    """An error occurred while checking for software updates."""
+
+    pass
+
+
+def _version_from_metadata() -> Optional[Version]:
+    try:
+        return Version(importlib.metadata.version("ms2rescore"))
+    except importlib.metadata.PackageNotFoundError:
+        return None
+
+
+def _version_from_pyproject() -> Optional[Version]:
+    pyproject = Path(__file__).resolve().parents[1] / "pyproject.toml"
+    if not pyproject.is_file():
+        return None
+
+    try:
+        data = toml.loads(pyproject.read_text(encoding="utf-8"))
+    except (OSError, ValueError):
+        return None
+
+    project = data.get("project") if isinstance(data, dict) else None
+    if isinstance(project, dict):
+        ver = project.get("version")
+        if isinstance(ver, str):
+            return Version(ver)
+    return None
+
+
+def _get_latest_version(timeout_seconds: float) -> Tuple[Version, Optional[str]]:
+    """Check GitHub latest release and return the version string."""
+    # Prepare GitHub API request
+    url = f"https://api.github.com/repos/{_GITHUB_REPO}/releases/latest"
+    user_agent = "ms2rescore/ (+https://github.com/compomics/ms2rescore)"
+    req = Request(url, headers={"Accept": "application/vnd.github+json", "User-Agent": user_agent})
+
+    # Fetch and parse release info
+    try:
+        with urlopen(req, timeout=timeout_seconds) as resp:
+            raw = resp.read()
+        data = json.loads(raw.decode("utf-8", errors="replace")) if raw else {}
+    except HTTPError as e:
+        raise UpdateCheckError(f"HTTP {e.code}") from e
+    except URLError as e:
+        raise UpdateCheckError("Network unavailable or timed out") from e
+    except Exception as e:
+        raise UpdateCheckError("Failed to fetch release info") from e
+
+    tag = data.get("tag_name") or data.get("name") or ""
+    if not tag:
+        raise UpdateCheckError("Latest release tag not found in API response")
+
+    # Validate version string
+    try:
+        latest_version = Version(tag)
+    except Exception as e:
+        raise UpdateCheckError("Latest release tag is not a valid version") from e
+
+    return latest_version, data.get("html_url") or data.get("url")
+
+
+def get_version() -> str:
+    """Return the version of this MS²Rescore installation."""
+    version = _version_from_metadata() or _version_from_pyproject() or "0+unknown"
+    return str(version)
+
+
+def check_for_update(
+    timeout_seconds: Optional[float] = None,
+) -> Dict[str, Optional[Union[str, bool]]]:
+    """Check GitHub latest release and report whether an update exists."""
+    timeout_seconds = timeout_seconds or _GITHUB_TIMEOUT_SECONDS
+
+    # Initialize result dictionary
+    result: Dict[str, Optional[Union[str, bool]]] = {
+        "update_available": False,
+        "current_version": None,
+        "latest_version": None,
+        "html_url": None,
+    }
+
+    # Get current version
+    current_version = _version_from_metadata() or _version_from_pyproject()
+    if current_version is None:
+        LOGGER.warning("Update check failed: Cannot determine current version")
+        return result
+    result["current_version"] = str(current_version)
+
+    # Get latest version from GitHub
+    try:
+        latest_version, html_url = _get_latest_version(timeout_seconds)
+    except UpdateCheckError as e:
+        LOGGER.warning("Update check failed: %s", e)
+        return result
+    result["latest_version"] = str(latest_version)
+    result["html_url"] = html_url
+
+    try:
+        result["update_available"] = latest_version > current_version
+    except Exception:
+        # If current_version can't be parsed, don't treat as updateable
+        result["update_available"] = False
+    return result

{ms2rescore-3.2.0.dev2 → ms2rescore-3.2.0.post1}/ms2rescore/config_parser.py

@@ -3,6 +3,7 @@
 import importlib.resources
 import json
 import multiprocessing as mp
+import re
 from argparse import Namespace
 from pathlib import Path
 from typing import Dict, List, Union
@@ -10,7 +11,7 @@ from typing import Dict, List, Union
 try:
     import tomllib
 except ImportError:
-    import tomli as tomllib
+    import tomli as tomllib  # type: ignore
 
 from cascade_config import CascadeConfig
 
@@ -86,6 +87,36 @@ def _validate_processes(config: Dict) -> Dict:
     return config
 
 
+def _validate_regular_expressions(config: Dict) -> Dict:
+    """Validate regular expressions in configuration."""
+    for field in [
+        "psm_id_pattern",
+        "spectrum_id_pattern",
+        "psm_id_rt_pattern",
+        "psm_id_im_pattern",
+    ]:
+        if config["ms2rescore"][field]:
+
+            # Check if valid regex
+            try:
+                pattern = re.compile(config["ms2rescore"][field])
+            except re.error as e:
+                raise MS2RescoreConfigurationError(
+                    f"Invalid regular expression provided for '{field}': {e}"
+                ) from e
+
+            # Check if regex has exactly one capturing group
+            if pattern.groups != 1:
+                raise MS2RescoreConfigurationError(
+                    f"Regular expression for '{field}' should contain exactly one "
+                    "capturing group. Please check and try again. "
+                    "See https://ms2rescore.readthedocs.io/en/stable/userguide/configuration/#mapping-psms-to-spectra "
+                    "for more information."
+                )
+
+    return config
+
+
 def parse_configurations(configurations: List[Union[dict, str, Path, Namespace]]) -> Dict:
     """
     Parse and validate MS²Rescore configuration files and CLI arguments.
@@ -142,6 +173,7 @@ def parse_configurations(configurations: List[Union[dict, str, Path, Namespace]]
     # Validate and infer filenames and number of parallel processes
     config = _validate_filenames(config)
     config = _validate_processes(config)
+    config = _validate_regular_expressions(config)
 
     # Convert feature_generators and rescoring_engine names to lowercase
     config["ms2rescore"]["feature_generators"] = {

{ms2rescore-3.2.0.dev2 → ms2rescore-3.2.0.post1}/ms2rescore/core.py

@@ -61,8 +61,16 @@ def rescore(configuration: Dict, psm_list: Optional[PSMList] = None) -> None:
     )
 
     # Add missing precursor info from spectrum file if needed
+    required_ms_data = {
+        ms_data
+        for fgen_name in config["feature_generators"].keys()
+        for ms_data in FEATURE_GENERATORS[fgen_name].required_ms_data
+    }
     available_ms_data = add_precursor_values(
-        psm_list, config["spectrum_path"], config["spectrum_id_pattern"]
+        psm_list,
+        required_ms_data,
+        spectrum_path=config["spectrum_path"],
+        spectrum_id_pattern=config["spectrum_id_pattern"],
     )
 
     # Add rescoring features