pyonsite 0.0.1__tar.gz

pyonsite-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 BigBio Stack
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyonsite-0.0.1/PKG-INFO

@@ -0,0 +1,337 @@
+Metadata-Version: 2.4
+Name: pyonsite
+Version: 0.0.1
+Summary: onsite: mass spectrometry post-translational localization tool
+License-Expression: MIT
+License-File: LICENSE
+Keywords: mass-spectrometry,proteomics,phosphorylation,ptm,ascore,phosphors
+Author: BigBio Stack
+Requires-Python: >=3.11
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Dist: click (>=8.0.0)
+Requires-Dist: numpy (>=2.3.2)
+Requires-Dist: pyopenms (>=3.4.0)
+Requires-Dist: scipy (>=1.16.1)
+Project-URL: Documentation, https://github.com/bigbio/onsite
+Project-URL: Homepage, https://github.com/bigbio/onsite
+Project-URL: Repository, https://github.com/bigbio/onsite
+Description-Content-Type: text/markdown
+
+# onsite
+
+[![Python application](https://github.com/bigbio/onsite/actions/workflows/python-app.yml/badge.svg?branch=main)](https://github.com/bigbio/onsite/actions/workflows/python-app.yml)
+![PyPI - Version](https://img.shields.io/pypi/v/onsite?style=flat)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/onsite)
+![Pepy Total Downloads](https://img.shields.io/pepy/dt/onsite)
+![GitHub Repo stars](https://img.shields.io/github/stars/bigbio/onsite)
+
+## What is onsite?
+
+**onsite** is a comprehensive Python package for mass spectrometry post-translational modification (PTM) localization. It provides algorithms for confident phosphorylation site localization and scoring, including implementations of AScore, PhosphoRS, and LucXor (LuciPHOr2).
+
+### Key Features
+
+- **Multiple Algorithms**: AScore, PhosphoRS, and LucXor implementations
+- **Statistical Validation**: Probability-based scoring with FLR estimation
+- **Unified CLI**: Single command-line interface for all algorithms
+- **Multi-threading**: Parallel processing for improved performance
+- **PyOpenMS Integration**: Seamless integration with the OpenMS ecosystem
+- **High Accuracy**: Confident site localization with statistical validation
+- **Flexible API**: Both command-line and Python API support
+
+## Supported Algorithms
+
+onsite provides three complementary algorithms for PTM localization:
+
+### 1. **AScore Algorithm**
+- **Method**: Probability-based approach using binomial statistics
+- **Features**: Site-determining ion analysis, fast processing
+- **Output**: AScore values indicating localization confidence
+- **Citation**: Beausoleil et al. (2006) *Nature Biotechnology*
+
+### 2. **PhosphoRS Algorithm**
+- **Method**: Compomics-style scoring with isomer analysis
+- **Features**: Site-specific probabilities, detailed isomer analysis
+- **Output**: Site probability scores and isomer details
+- **Citation**: Taus et al. (2011) *Journal of Proteome Research*
+
+### 3. **LucXor (LuciPHOr2) Algorithm**
+- **Method**: Two-stage processing with FLR estimation
+- **Features**: False localization rate calculation, decoy-based validation
+- **Output**: Delta scores, peptide scores, global and local FLR
+- **Citation**: Fermin et al. (2013, 2015) *MCP* and *Bioinformatics*
+
+## Installation
+
+### Prerequisites
+
+- Python 3.11+
+- PyOpenMS 3.4.0+
+- NumPy 2.3.2+
+- SciPy 1.16.1+
+
+### Using Poetry (Recommended)
+
+```bash
+# Clone the repository
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+
+# Install with Poetry
+poetry install
+
+# Activate the virtual environment
+poetry shell
+```
+
+### Using pip
+
+```bash
+# Install from PyPI (note: PyPI package name is 'pyonsite')
+pip install pyonsite
+
+# Or install from source
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+pip install -e .
+```
+
+**Note:** The package is published on PyPI as `pyonsite` due to a naming conflict, but the module is still imported as `onsite`.
+
+### Development Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+
+# Install with development dependencies
+poetry install --with dev
+
+# Or with pip
+pip install -e ".[dev]"
+```
+
+## Usage
+
+### Command Line Interface
+
+onsite provides a unified command-line interface for all algorithms:
+
+#### Unified onsite CLI
+
+```bash
+# AScore algorithm
+onsite ascore -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# PhosphoRS algorithm  
+onsite phosphors -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# LucXor algorithm
+onsite lucxor -in spectra.mzML -id identifications.idXML -out results.idXML
+```
+
+#### Individual Pipeline Tools
+
+##### AScore Pipeline
+
+```bash
+# Basic usage
+python -m onsite.ascore.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.ascore.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-mass-tolerance 0.05 \
+    --fragment-mass-unit Da \
+    --threads 4 \
+    --add-decoys
+```
+
+##### PhosphoRS Pipeline
+
+```bash
+# Basic usage
+python -m onsite.phosphors.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.phosphors.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-mass-tolerance 0.05 \
+    --fragment-mass-unit Da \
+    --threads 1 \
+    --add-decoys
+```
+
+##### LucXor Pipeline
+
+```bash
+# Basic usage
+python -m onsite.lucxor.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.lucxor.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-method HCD \
+    --fragment-mass-tolerance 0.5 \
+    --fragment-error-units Da \
+    --threads 8 \
+    --debug
+```
+
+### Command-line Options
+
+#### AScore Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-mass-tolerance` | 0.05 | Fragment mass tolerance |
+| `--fragment-mass-unit` | Da | Tolerance unit (Da or ppm) |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--add-decoys` | False | Include decoy sites for validation |
+| `--debug` | False | Enable debug logging |
+
+#### PhosphoRS Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-mass-tolerance` | 0.05 | Fragment mass tolerance |
+| `--fragment-mass-unit` | Da | Tolerance unit (Da or ppm) |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--add-decoys` | False | Include decoy sites for validation |
+| `--debug` | False | Enable debug logging |
+
+#### LucXor Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-method` | CID | Fragmentation method (CID or HCD) |
+| `--fragment-mass-tolerance` | 0.5 | Fragment mass tolerance |
+| `--fragment-error-units` | Da | Tolerance units (Da or ppm) |
+| `--min-mz` | 150.0 | Minimum m/z value to consider |
+| `--target-modifications` | Phospho (S/T/Y) | List of target PTM definitions |
+| `--neutral-losses` | sty -H3PO4 -97.97690 | Neutral loss definitions applied during scoring |
+| `--decoy-mass` | 79.966331 | Mass offset used when generating decoy permutations |
+| `--decoy-neutral-losses` | X -H3PO4 -97.97690 | Neutral loss patterns for decoy permutations |
+| `--max-charge-state` | 5 | Maximum charge state |
+| `--max-peptide-length` | 40 | Maximum peptide length |
+| `--max-num-perm` | 16384 | Maximum permutations |
+| `--modeling-score-threshold` | 0.95 | Minimum score for selecting PSMs during model building |
+| `--scoring-threshold` | 0.0 | Minimum LucXor score to report |
+| `--min-num-psms-model` | 50 | Minimum number of high-scoring PSMs required for modeling |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--rt-tolerance` | 0.01 | RT tolerance used when matching spectra by retention time |
+| `--debug` | False | Enable debug logging |
+
+## Algorithm Details
+
+### AScore Algorithm
+
+The AScore algorithm provides phosphorylation site localization by analyzing MS/MS fragment ions to identify site-determining ions and computing localization probabilities based on fragment evidence.
+
+**Output Metrics:**
+
+- `AScore_pep_score`: Overall peptide score
+- `AScore_1, AScore_2, ...`: Individual site scores
+- `ProForma`: Standardized sequence notation with confidence scores
+
+### PhosphoRS Algorithm
+
+The PhosphoRS algorithm implements a comprehensive approach using isomer generation, theoretical spectrum matching, and probability scoring for confident phosphorylation site assignment.
+
+**Output Metrics:**
+- Site-specific probability scores (0-100%)
+- Isomer details with sequence and score
+- Detailed confidence metrics
+
+### LucXor (LuciPHOr2) Algorithm
+
+LucXor implements the complete LuciPHOr2 algorithm with two-stage processing for accurate PTM localization with false localization rate (FLR) estimation.
+
+**Output Metrics:**
+- `Luciphor_delta_score`: Main localization score
+- `Luciphor_pep_score`: Peptide identification score
+- `Luciphor_global_flr`: Global false localization rate
+- `Luciphor_local_flr`: Local false localization rate
+
+## Example Results
+
+You can find example result files in the `data` directory. Here are the direct links to different algorithm result files:
+
+| Algorithm | Description | Result File |
+|---|---|---|
+| AScore | AScore phosphorylation site localization results | [AScore Example](data/1_ascore_result.idXML) |
+| PhosphoRS | PhosphoRS phosphorylation site localization results | [PhosphoRS Example](data/1_phosphors_result.idXML) |
+| LucXor | LucXor (LuciPHOr2) PTM localization results with FLR | [LucXor Example](data/1_lucxor_result.idXML) |
+
+## Documentation
+
+For more detailed information:
+
+- [AScore Algorithm Documentation](docs/algorithms/ascore.md)
+- [PhosphoRS Algorithm Documentation](docs/algorithms/phosphors.md)
+- [LucXor Algorithm Documentation](docs/algorithms/lucxor.md)
+- [Citations and References](docs/citations.md)
+
+## Contributing
+
+To contribute to onsite:
+
+1. Fork the repository
+2. Clone your fork: `git clone https://github.com/YOUR-USERNAME/onsite`
+3. Create a feature branch: `git checkout -b new-feature`
+4. Make your changes
+5. Install in development mode: `pip install -e .`
+6. Test your changes: `poetry run pytest`
+7. Commit your changes: `git commit -am 'Add new feature'`
+8. Push to the branch: `git push origin new-feature`
+9. Submit a pull request
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use onsite in your research, please cite:
+
+```text
+onsite: Mass spectrometry post-translational modification localization tool. 
+https://github.com/bigbio/onsite
+```
+
+## Related Tools
+
+- [PyOpenMS](https://pyopenms.readthedocs.io/) - Python bindings for OpenMS
+- [OpenMS](https://www.openms.de/) - Open-source tools for mass spectrometry
+- [nf-core/quantms](https://nf-co.re/quantms) - Quantitative mass spectrometry workflow
+
+## Need Help?
+
+If you have questions or need assistance:
+- [Open an issue](https://github.com/bigbio/onsite/issues) on GitHub
+- Check [existing issues](https://github.com/bigbio/onsite/issues?q=is%3Aissue) for solutions
+
+## Acknowledgments
+
+onsite builds upon the excellent work of the original algorithm developers and the OpenMS community. We thank all contributors and users for their feedback and support.
+
+---
+
+
+
+

pyonsite-0.0.1/README.md

@@ -0,0 +1,309 @@
+# onsite
+
+[![Python application](https://github.com/bigbio/onsite/actions/workflows/python-app.yml/badge.svg?branch=main)](https://github.com/bigbio/onsite/actions/workflows/python-app.yml)
+![PyPI - Version](https://img.shields.io/pypi/v/onsite?style=flat)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/onsite)
+![Pepy Total Downloads](https://img.shields.io/pepy/dt/onsite)
+![GitHub Repo stars](https://img.shields.io/github/stars/bigbio/onsite)
+
+## What is onsite?
+
+**onsite** is a comprehensive Python package for mass spectrometry post-translational modification (PTM) localization. It provides algorithms for confident phosphorylation site localization and scoring, including implementations of AScore, PhosphoRS, and LucXor (LuciPHOr2).
+
+### Key Features
+
+- **Multiple Algorithms**: AScore, PhosphoRS, and LucXor implementations
+- **Statistical Validation**: Probability-based scoring with FLR estimation
+- **Unified CLI**: Single command-line interface for all algorithms
+- **Multi-threading**: Parallel processing for improved performance
+- **PyOpenMS Integration**: Seamless integration with the OpenMS ecosystem
+- **High Accuracy**: Confident site localization with statistical validation
+- **Flexible API**: Both command-line and Python API support
+
+## Supported Algorithms
+
+onsite provides three complementary algorithms for PTM localization:
+
+### 1. **AScore Algorithm**
+- **Method**: Probability-based approach using binomial statistics
+- **Features**: Site-determining ion analysis, fast processing
+- **Output**: AScore values indicating localization confidence
+- **Citation**: Beausoleil et al. (2006) *Nature Biotechnology*
+
+### 2. **PhosphoRS Algorithm**
+- **Method**: Compomics-style scoring with isomer analysis
+- **Features**: Site-specific probabilities, detailed isomer analysis
+- **Output**: Site probability scores and isomer details
+- **Citation**: Taus et al. (2011) *Journal of Proteome Research*
+
+### 3. **LucXor (LuciPHOr2) Algorithm**
+- **Method**: Two-stage processing with FLR estimation
+- **Features**: False localization rate calculation, decoy-based validation
+- **Output**: Delta scores, peptide scores, global and local FLR
+- **Citation**: Fermin et al. (2013, 2015) *MCP* and *Bioinformatics*
+
+## Installation
+
+### Prerequisites
+
+- Python 3.11+
+- PyOpenMS 3.4.0+
+- NumPy 2.3.2+
+- SciPy 1.16.1+
+
+### Using Poetry (Recommended)
+
+```bash
+# Clone the repository
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+
+# Install with Poetry
+poetry install
+
+# Activate the virtual environment
+poetry shell
+```
+
+### Using pip
+
+```bash
+# Install from PyPI (note: PyPI package name is 'pyonsite')
+pip install pyonsite
+
+# Or install from source
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+pip install -e .
+```
+
+**Note:** The package is published on PyPI as `pyonsite` due to a naming conflict, but the module is still imported as `onsite`.
+
+### Development Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/bigbio/onsite.git
+cd onsite
+
+# Install with development dependencies
+poetry install --with dev
+
+# Or with pip
+pip install -e ".[dev]"
+```
+
+## Usage
+
+### Command Line Interface
+
+onsite provides a unified command-line interface for all algorithms:
+
+#### Unified onsite CLI
+
+```bash
+# AScore algorithm
+onsite ascore -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# PhosphoRS algorithm  
+onsite phosphors -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# LucXor algorithm
+onsite lucxor -in spectra.mzML -id identifications.idXML -out results.idXML
+```
+
+#### Individual Pipeline Tools
+
+##### AScore Pipeline
+
+```bash
+# Basic usage
+python -m onsite.ascore.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.ascore.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-mass-tolerance 0.05 \
+    --fragment-mass-unit Da \
+    --threads 4 \
+    --add-decoys
+```
+
+##### PhosphoRS Pipeline
+
+```bash
+# Basic usage
+python -m onsite.phosphors.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.phosphors.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-mass-tolerance 0.05 \
+    --fragment-mass-unit Da \
+    --threads 1 \
+    --add-decoys
+```
+
+##### LucXor Pipeline
+
+```bash
+# Basic usage
+python -m onsite.lucxor.cli -in spectra.mzML -id identifications.idXML -out results.idXML
+
+# With custom parameters
+python -m onsite.lucxor.cli -in spectra.mzML -id identifications.idXML -out results.idXML \
+    --fragment-method HCD \
+    --fragment-mass-tolerance 0.5 \
+    --fragment-error-units Da \
+    --threads 8 \
+    --debug
+```
+
+### Command-line Options
+
+#### AScore Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-mass-tolerance` | 0.05 | Fragment mass tolerance |
+| `--fragment-mass-unit` | Da | Tolerance unit (Da or ppm) |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--add-decoys` | False | Include decoy sites for validation |
+| `--debug` | False | Enable debug logging |
+
+#### PhosphoRS Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-mass-tolerance` | 0.05 | Fragment mass tolerance |
+| `--fragment-mass-unit` | Da | Tolerance unit (Da or ppm) |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--add-decoys` | False | Include decoy sites for validation |
+| `--debug` | False | Enable debug logging |
+
+#### LucXor Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-in` | - | Input mzML file with spectra |
+| `-id` | - | Input idXML file with identifications |
+| `-out` | - | Output idXML file with scores |
+| `--fragment-method` | CID | Fragmentation method (CID or HCD) |
+| `--fragment-mass-tolerance` | 0.5 | Fragment mass tolerance |
+| `--fragment-error-units` | Da | Tolerance units (Da or ppm) |
+| `--min-mz` | 150.0 | Minimum m/z value to consider |
+| `--target-modifications` | Phospho (S/T/Y) | List of target PTM definitions |
+| `--neutral-losses` | sty -H3PO4 -97.97690 | Neutral loss definitions applied during scoring |
+| `--decoy-mass` | 79.966331 | Mass offset used when generating decoy permutations |
+| `--decoy-neutral-losses` | X -H3PO4 -97.97690 | Neutral loss patterns for decoy permutations |
+| `--max-charge-state` | 5 | Maximum charge state |
+| `--max-peptide-length` | 40 | Maximum peptide length |
+| `--max-num-perm` | 16384 | Maximum permutations |
+| `--modeling-score-threshold` | 0.95 | Minimum score for selecting PSMs during model building |
+| `--scoring-threshold` | 0.0 | Minimum LucXor score to report |
+| `--min-num-psms-model` | 50 | Minimum number of high-scoring PSMs required for modeling |
+| `--threads` | 1 | Number of threads for parallel processing |
+| `--rt-tolerance` | 0.01 | RT tolerance used when matching spectra by retention time |
+| `--debug` | False | Enable debug logging |
+
+## Algorithm Details
+
+### AScore Algorithm
+
+The AScore algorithm provides phosphorylation site localization by analyzing MS/MS fragment ions to identify site-determining ions and computing localization probabilities based on fragment evidence.
+
+**Output Metrics:**
+
+- `AScore_pep_score`: Overall peptide score
+- `AScore_1, AScore_2, ...`: Individual site scores
+- `ProForma`: Standardized sequence notation with confidence scores
+
+### PhosphoRS Algorithm
+
+The PhosphoRS algorithm implements a comprehensive approach using isomer generation, theoretical spectrum matching, and probability scoring for confident phosphorylation site assignment.
+
+**Output Metrics:**
+- Site-specific probability scores (0-100%)
+- Isomer details with sequence and score
+- Detailed confidence metrics
+
+### LucXor (LuciPHOr2) Algorithm
+
+LucXor implements the complete LuciPHOr2 algorithm with two-stage processing for accurate PTM localization with false localization rate (FLR) estimation.
+
+**Output Metrics:**
+- `Luciphor_delta_score`: Main localization score
+- `Luciphor_pep_score`: Peptide identification score
+- `Luciphor_global_flr`: Global false localization rate
+- `Luciphor_local_flr`: Local false localization rate
+
+## Example Results
+
+You can find example result files in the `data` directory. Here are the direct links to different algorithm result files:
+
+| Algorithm | Description | Result File |
+|---|---|---|
+| AScore | AScore phosphorylation site localization results | [AScore Example](data/1_ascore_result.idXML) |
+| PhosphoRS | PhosphoRS phosphorylation site localization results | [PhosphoRS Example](data/1_phosphors_result.idXML) |
+| LucXor | LucXor (LuciPHOr2) PTM localization results with FLR | [LucXor Example](data/1_lucxor_result.idXML) |
+
+## Documentation
+
+For more detailed information:
+
+- [AScore Algorithm Documentation](docs/algorithms/ascore.md)
+- [PhosphoRS Algorithm Documentation](docs/algorithms/phosphors.md)
+- [LucXor Algorithm Documentation](docs/algorithms/lucxor.md)
+- [Citations and References](docs/citations.md)
+
+## Contributing
+
+To contribute to onsite:
+
+1. Fork the repository
+2. Clone your fork: `git clone https://github.com/YOUR-USERNAME/onsite`
+3. Create a feature branch: `git checkout -b new-feature`
+4. Make your changes
+5. Install in development mode: `pip install -e .`
+6. Test your changes: `poetry run pytest`
+7. Commit your changes: `git commit -am 'Add new feature'`
+8. Push to the branch: `git push origin new-feature`
+9. Submit a pull request
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use onsite in your research, please cite:
+
+```text
+onsite: Mass spectrometry post-translational modification localization tool. 
+https://github.com/bigbio/onsite
+```
+
+## Related Tools
+
+- [PyOpenMS](https://pyopenms.readthedocs.io/) - Python bindings for OpenMS
+- [OpenMS](https://www.openms.de/) - Open-source tools for mass spectrometry
+- [nf-core/quantms](https://nf-co.re/quantms) - Quantitative mass spectrometry workflow
+
+## Need Help?
+
+If you have questions or need assistance:
+- [Open an issue](https://github.com/bigbio/onsite/issues) on GitHub
+- Check [existing issues](https://github.com/bigbio/onsite/issues?q=is%3Aissue) for solutions
+
+## Acknowledgments
+
+onsite builds upon the excellent work of the original algorithm developers and the OpenMS community. We thank all contributors and users for their feedback and support.
+
+---
+
+
+

pyonsite-0.0.1/onsite/__init__.py

@@ -0,0 +1,27 @@
+"""
+OnSite: Mass spectrometry post-translational modification localization tool.
+
+This package provides tools for phosphorylation site localization and scoring
+using various algorithms including AScore, PhosphoRS, and LucXor.
+"""
+
+__version__ = "0.0.1"
+__author__ = "BigBio Stack"
+__license__ = "MIT"
+
+# Import main modules
+from .ascore import AScore
+from .phosphors import calculate_phospho_localization_compomics_style
+
+# Import LucXor components
+try:
+    from . import lucxor
+
+    LUCXOR_AVAILABLE = True
+except ImportError:
+    LUCXOR_AVAILABLE = False
+
+__all__ = ["AScore", "calculate_phospho_localization_compomics_style"]
+
+if LUCXOR_AVAILABLE:
+    __all__.extend(["lucxor"])

pyonsite-0.0.1/onsite/ascore/__init__.py

@@ -0,0 +1,10 @@
+"""
+AScore package for phosphorylation site localization.
+
+This package provides the AScore algorithm implementation for mass spectrometry
+post-translational modification localization.
+"""
+
+from .ascore import AScore
+
+__all__ = ["AScore"]