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
pip install debase
Quick Start
# 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
-vfor 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
1 maintainer
Metadata
1 maintainer
Release files for debase 2.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| debase-2.1.0.tar.gz | 962.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| debase-2.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / debase-2.1.0.tar.gz
| Download URL | debase-2.1.0.tar.gz |
|---|---|
| Size | 962.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
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Release files / debase-2.1.0-py3-none-any.whl
| Download URL | debase-2.1.0-py3-none-any.whl |
|---|---|
| Size | 173.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.13.2
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