debase 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

debase-0.4.3.dist-info/METADATA

@@ -1,296 +0,0 @@
-Metadata-Version: 2.4
-Name: debase
-Version: 0.4.3
-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
-
-Enzyme lineage analysis and sequence extraction package with advanced parallel processing capabilities.
-
-## Installation
-
-### Quick Install (PyPI)
-```bash
-pip install debase
-```
-
-### Development Setup with Conda (Recommended)
-
-1. **Clone the repository**
-```bash
-git clone https://github.com/YuemingLong/DEBase.git
-cd DEBase
-```
-
-2. **Create conda environment from provided file**
-```bash
-conda env create -f environment.yml
-conda activate debase
-```
-
-3. **Install DEBase in development mode**
-```bash
-pip install -e .
-```
-
-### Manual Setup
-
-If you prefer to set up the environment manually:
-
-```bash
-# Create new conda environment
-conda create -n debase python=3.9
-conda activate debase
-
-# Install conda packages
-conda install -c conda-forge pandas numpy matplotlib seaborn jupyter jupyterlab openpyxl biopython requests tqdm
-
-# Install RDKit (optional - used for SMILES canonicalization)
-conda install -c conda-forge rdkit
-
-# Install pip-only packages
-pip install PyMuPDF google-generativeai debase
-```
-
-**Note about RDKit**: RDKit is optional and only used for canonicalizing SMILES strings in the output. If not installed, DEBase will still function normally but SMILES strings won't be standardized.
-
-## Requirements
-
-- Python 3.8 or higher
-- A Gemini API key (set as environment variable `GEMINI_API_KEY`)
-
-### Setting up Gemini API Key
-
-```bash
-# Option 1: Export in your shell
-export GEMINI_API_KEY="your-api-key-here"
-
-# Option 2: Add to ~/.bashrc or ~/.zshrc for persistence
-echo 'export GEMINI_API_KEY="your-api-key-here"' >> ~/.bashrc
-source ~/.bashrc
-
-# Option 3: Create .env file in project directory
-echo 'GEMINI_API_KEY=your-api-key-here' > .env
-```
-
-## Recent Updates
-
-- **Campaign-Aware Extraction**: Automatically detects and processes multiple directed evolution campaigns in a single paper
-- **Improved Model Support**: Updated to use stable Gemini models for better reliability
-- **Enhanced PDB Integration**: Intelligent AI-based matching of PDB structures to enzyme variants
-- **Better Filtering**: Automatic removal of non-enzyme entries (buffers, controls, media)
-- **Optimized Performance**: Removed unnecessary rate limiting for faster processing
-- **External Sequence Fetching**: Automatic retrieval from PDB and UniProt databases when sequences aren't in papers
-- **Improved SI Processing**: Structure-aware extraction of supplementary information
-- **Vision Support**: Extracts data from figures and tables using multimodal AI capabilities
-
-## Quick Start
-
-### Basic Usage
-```bash
-# Run the full pipeline (sequential processing)
-debase --manuscript manuscript.pdf --si supplementary.pdf --output output.csv
-```
-
-### High-Performance Parallel Processing
-```bash
-# Use parallel individual processing for maximum speed + accuracy
-debase --manuscript manuscript.pdf --si supplementary.pdf --output output.csv \
-  --use-parallel-individual --max-workers 5
-
-# Use batch processing for maximum speed (slight accuracy trade-off)
-debase --manuscript manuscript.pdf --si supplementary.pdf --output output.csv \
-  --use-optimized-reaction --reaction-batch-size 5
-```
-
-## Processing Methods
-
-DEBase offers three processing approaches optimized for different use cases:
-
-### 1. **Parallel Individual Processing** (Recommended)
-- **42 individual API calls** (21 for reactions + 21 for substrate scope)
-- **5 calls running simultaneously** for 4-5x speedup
-- **Maximum accuracy** - each enzyme gets dedicated attention
-- **Best for:** Production use, important analyses
-
-```bash
-debase --manuscript paper.pdf --si si.pdf --use-parallel-individual --max-workers 5
-```
-
-### 2. **Batch Processing** (Fastest)
-- **~8 total API calls** (multiple enzymes per call)
-- **Fastest processing** - up to 8x speedup
-- **Good accuracy** - slight trade-off for complex chemical names
-- **Best for:** Quick analyses, large-scale processing
-
-```bash
-debase --manuscript paper.pdf --si si.pdf --use-optimized-reaction --reaction-batch-size 5
-```
-
-### 3. **Sequential Processing** (Most Accurate)
-- **42 sequential API calls** (one at a time)
-- **Highest accuracy** but slowest
-- **Best for:** Critical analyses, small datasets
-
-```bash
-debase --manuscript paper.pdf --si si.pdf  # Default method
-```
-
-
-## Advanced Usage
-
-### Skip Steps with Existing Data
-```bash
-# Skip lineage extraction if you already have it
-debase --manuscript paper.pdf --si si.pdf --output output.csv \
-  --skip-lineage --existing-lineage existing_lineage.csv \
-  --use-parallel-individual
-```
-
-### Direct Module Usage
-```bash
-# Run only reaction extraction with parallel processing
-python -m debase.reaction_info_extractor_parallel \
-  --manuscript paper.pdf --si si.pdf --lineage-csv lineage.csv \
-  --max-workers 5 --output reactions.csv
-
-# Run only substrate scope extraction with parallel processing  
-python -m debase.substrate_scope_extractor_parallel \
-  --manuscript paper.pdf --si si.pdf --lineage-csv lineage.csv \
-  --max-workers 5 --output substrate_scope.csv
-```
-## Pipeline Architecture
-
-The DEBase pipeline consists of 5 main steps:
-
-1. **Lineage Extraction** (Sequential) - Identifies all enzymes and their relationships
-   - Extracts mutation information and evolutionary paths
-   - Detects multiple directed evolution campaigns automatically
-   - Fetches sequences from external databases (PDB, UniProt)
-   - Filters out non-enzyme entries automatically
-2. **Sequence Cleanup** (Local) - Generates protein sequences from mutations  
-   - Applies mutations to parent sequences
-   - Handles complex mutations and domain modifications
-   - Validates sequence integrity
-3. **Reaction Extraction** (Parallel/Batch/Sequential) - Extracts reaction conditions and performance data
-   - Campaign-aware extraction for multi-lineage papers
-   - Vision-based extraction from figures and tables
-   - Automatic IUPAC name resolution
-4. **Substrate Scope Extraction** (Parallel/Sequential) - Finds additional substrates tested
-5. **Data Formatting** (Local) - Combines all data into final output
-
-## Features
-
-- **Multi-processing modes:** Sequential, parallel individual, and batch processing
-- **Campaign detection:** Automatically identifies and separates multiple directed evolution campaigns
-- **Intelligent error handling:** Automatic retries with exponential backoff
-- **External database integration:** Automatic sequence fetching from PDB and UniProt
-- **AI-powered matching:** Uses Gemini to intelligently match database entries to enzyme variants
-- **Smart filtering:** Automatically excludes non-enzyme entries (buffers, controls, etc.)
-- **Vision capabilities:** Extracts data from both text and images in PDFs
-
-## Complete Command Reference
-
-### Core Arguments
-```bash
---manuscript PATH           # Required: Path to manuscript PDF
---si PATH                  # Optional: Path to supplementary information PDF
---output PATH              # Output file path (default: manuscript_name_debase.csv)
-```
-
-### Performance Options
-```bash
---use-parallel-individual  # Use parallel processing (recommended)
---max-workers N            # Number of parallel workers (default: 5)
---use-optimized-reaction   # Use batch processing for speed
---reaction-batch-size N    # Enzymes per batch (default: 5)
---no-parallel-queries      # Disable parallel processing
-```
-
-### Pipeline Control
-```bash
---skip-lineage             # Skip lineage extraction step
---skip-sequence            # Skip sequence cleanup step  
---skip-reaction            # Skip reaction extraction step
---skip-substrate-scope     # Skip substrate scope extraction step
---skip-lineage-format      # Skip final formatting step
---skip-validation          # Skip data validation step
-```
-
-### Data Management
-```bash
---existing-lineage PATH    # Use existing lineage data
---existing-sequence PATH   # Use existing sequence data
---existing-reaction PATH   # Use existing reaction data
---keep-intermediates       # Preserve intermediate files
-```
-
-### Advanced Options
-```bash
---model-name NAME          # Gemini model to use
---max-retries N            # Maximum retry attempts (default: 2)
---max-chars N              # Max characters from PDFs (default: 75000)
---debug-dir PATH           # Directory for debug output (prompts, API responses)
-```
-
-## Tips for Best Performance
-
-1. **Use parallel individual processing** for the best balance of speed and accuracy
-2. **Set max-workers to 5** to avoid API rate limits while maximizing throughput
-3. **Use batch processing** only when speed is critical and some accuracy loss is acceptable
-4. **Skip validation** (`--skip-validation`) for faster processing in production
-5. **Keep intermediates** (`--keep-intermediates`) for debugging and incremental runs
-6. 
-

debase-0.4.3.dist-info/RECORD

@@ -1,16 +0,0 @@
-debase/__init__.py,sha256=YeKveGj_8fwuu5ozoK2mUU86so_FjiCwsvg1d_lYVZU,586
-debase/__main__.py,sha256=LbxYt2x9TG5Ced7LpzzX_8gkWyXeZSlVHzqHfqAiPwQ,160
-debase/_version.py,sha256=r0b4fvQcrrvOScFMddjVgWAGNt17iQxCJH2xYW06jio,49
-debase/build_db.py,sha256=bW574GxsL1BJtDwM19urLbciPcejLzfraXZPpzm09FQ,7167
-debase/cleanup_sequence.py,sha256=4qZrSXInyJKEJqcgcONp4IX24ALEj5lf7E0XaOZVxZ0,40329
-debase/enzyme_lineage_extractor.py,sha256=tFyrcWkNKKr8T9xq0tIXUDNfcX0tbdWGrLhgo5m7lmA,129804
-debase/lineage_format.py,sha256=Q6kpqKPUxJsMYpb0Yt8IbVlp6VDYX2vkITuGhT9MEbw,47056
-debase/reaction_info_extractor.py,sha256=q-iHgfVLXP4r2Se8yA9I0AvtnAhHBltTztrXspl3EKU,151949
-debase/substrate_scope_extractor.py,sha256=eaVimhxmmaRj-9dRN6RKK4yStCmZAuX8xBaarsIsmUo,114212
-debase/wrapper.py,sha256=r0xxoiBvmMIktiGPOD4w9hne8m0SLzZ03WeWnBuDW0A,25236
-debase-0.4.3.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
-debase-0.4.3.dist-info/METADATA,sha256=UT8ymX3oothXvgA9ayr74_Bd-St7I0Pj7CoEg8LlKg8,10789
-debase-0.4.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-debase-0.4.3.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
-debase-0.4.3.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
-debase-0.4.3.dist-info/RECORD,,