debase 0.4.3__tar.gz → 0.4.4__tar.gz

debase-0.4.4/PKG-INFO

@@ -0,0 +1,121 @@
+Metadata-Version: 2.4
+Name: debase
+Version: 0.4.4
+Summary: Enzyme lineage analysis and sequence extraction package
+Home-page: https://github.com/YuemingLong/DEBase
+Author: DEBase Team
+Author-email: DEBase Team <ylong@caltech.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/YuemingLong/DEBase
+Project-URL: Documentation, https://github.com/YuemingLong/DEBase#readme
+Project-URL: Repository, https://github.com/YuemingLong/DEBase
+Project-URL: Issues, https://github.com/YuemingLong/DEBase/issues
+Classifier: Development Status :: 4 - Beta
+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 :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.0.0
+Requires-Dist: PyMuPDF>=1.18.0
+Requires-Dist: numpy>=1.19.0
+Requires-Dist: google-generativeai>=0.3.0
+Requires-Dist: biopython>=1.78
+Requires-Dist: requests>=2.25.0
+Requires-Dist: httpx>=0.24.0
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: openpyxl>=3.0.0
+Requires-Dist: PyPDF2>=2.0.0
+Requires-Dist: Pillow>=8.0.0
+Requires-Dist: networkx>=2.5
+Provides-Extra: rdkit
+Requires-Dist: rdkit>=2020.03.1; extra == "rdkit"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# DEBase
+
+DEBase is a Python package for extracting and analyzing enzyme lineage data from scientific papers using AI-powered parsing.
+
+## Features
+
+- Extract enzyme variant lineages from PDF documents
+- Parse protein and DNA sequences with mutation annotations
+- Extract reaction performance metrics (yield, TTN, ee)
+- Extract and organize substrate scope data
+- Match enzyme variants across different data sources using AI
+- Generate structured CSV outputs for downstream analysis
+
+## Installation
+
+```bash
+pip install debase
+```
+
+## Quick Start
+
+```bash
+# Run the complete pipeline
+debase --manuscript paper.pdf --si supplementary.pdf --output results.csv
+
+# Enable debug mode to save Gemini prompts and responses
+debase --manuscript paper.pdf --si supplementary.pdf --output results.csv --debug-dir ./debug_output
+
+# Individual components with debugging
+python -m debase.enzyme_lineage_extractor --manuscript paper.pdf --output lineage.csv --debug-dir ./debug_output
+python -m debase.reaction_info_extractor --manuscript paper.pdf --lineage-csv lineage.csv --output reactions.csv --debug-dir ./debug_output
+python -m debase.substrate_scope_extractor --manuscript paper.pdf --lineage-csv lineage.csv --output substrate_scope.csv --debug-dir ./debug_output
+python -m debase.lineage_format -r reactions.csv -s substrate_scope.csv -o final.csv -v
+```
+
+## Debugging
+
+Use the `--debug-dir` flag to save all Gemini API prompts and responses for debugging:
+- Location extraction prompts
+- Sequence extraction prompts (can be very large, up to 150K characters)
+- Enzyme matching prompts
+- All API responses with timestamps
+- Note: lineage_format.py uses `-v` for verbose output instead of `--debug-dir`
+
+## Requirements
+
+- Python 3.8+
+- Google Gemini API key (set as GEMINI_API_KEY environment variable)
+
+## Version
+
+0.4.4
+
+## License
+
+MIT License
+
+## Authors
+
+DEBase Team - Caltech
+
+## Contact
+
+ylong@caltech.edu

debase-0.4.4/README.md

@@ -0,0 +1,64 @@
+# DEBase
+
+DEBase is a Python package for extracting and analyzing enzyme lineage data from scientific papers using AI-powered parsing.
+
+## Features
+
+- Extract enzyme variant lineages from PDF documents
+- Parse protein and DNA sequences with mutation annotations
+- Extract reaction performance metrics (yield, TTN, ee)
+- Extract and organize substrate scope data
+- Match enzyme variants across different data sources using AI
+- Generate structured CSV outputs for downstream analysis
+
+## Installation
+
+```bash
+pip install debase
+```
+
+## Quick Start
+
+```bash
+# Run the complete pipeline
+debase --manuscript paper.pdf --si supplementary.pdf --output results.csv
+
+# Enable debug mode to save Gemini prompts and responses
+debase --manuscript paper.pdf --si supplementary.pdf --output results.csv --debug-dir ./debug_output
+
+# Individual components with debugging
+python -m debase.enzyme_lineage_extractor --manuscript paper.pdf --output lineage.csv --debug-dir ./debug_output
+python -m debase.reaction_info_extractor --manuscript paper.pdf --lineage-csv lineage.csv --output reactions.csv --debug-dir ./debug_output
+python -m debase.substrate_scope_extractor --manuscript paper.pdf --lineage-csv lineage.csv --output substrate_scope.csv --debug-dir ./debug_output
+python -m debase.lineage_format -r reactions.csv -s substrate_scope.csv -o final.csv -v
+```
+
+## Debugging
+
+Use the `--debug-dir` flag to save all Gemini API prompts and responses for debugging:
+- Location extraction prompts
+- Sequence extraction prompts (can be very large, up to 150K characters)
+- Enzyme matching prompts
+- All API responses with timestamps
+- Note: lineage_format.py uses `-v` for verbose output instead of `--debug-dir`
+
+## Requirements
+
+- Python 3.8+
+- Google Gemini API key (set as GEMINI_API_KEY environment variable)
+
+## Version
+
+0.4.4
+
+## License
+
+MIT License
+
+## Authors
+
+DEBase Team - Caltech
+
+## Contact
+
+ylong@caltech.edu

{debase-0.4.3 → debase-0.4.4}/src/debase/_version.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "0.4.3"
+__version__ = "0.4.4"