# pLannotate-python
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://doi.org/10.1093/nar/gkab374)
<img width="400" alt="pLannotate_logo" src="plannotate/data/images/pLannotate.png">
**Automated annotation of engineered plasmids**
`pLannotate-python` is a Python package for automatically annotating engineered plasmids using sequence similarity searches against curated databases. Fast, parallel processing with automatic database setup.
## Features
- **Fast, parallel annotation**: Uses Diamond, BLAST, and Infernal concurrently
- **Multiple databases**: Protein (fpbase, swissprot), nucleotide (snapgene), RNA (Rfam)
- **Circular plasmid support**: Handles origin-crossing features
- **Automatic database setup**: Downloads and configures databases (~900MB)
- **Flexible output**: GenBank files, CSV reports, or pandas DataFrames
## Installation
```bash
# Install with uv (recommended)
uv add plannotate-python
# Or with pip
pip install plannotate-python
```
### External Tools Required
```bash
# macOS (Homebrew)
brew install diamond blast infernal ripgrep
# Linux (conda/mamba)
conda install -c bioconda diamond blast infernal ripgrep
# Ubuntu/Debian
sudo apt install diamond-aligner ncbi-blast+ infernal ripgrep
```
### SSL Certificate Fix (macOS)
If you encounter SSL certificate errors during database download:
```bash
# Replace X.Y with your Python version (e.g., 3.11)
open "/Applications/Python X.Y/Install Certificates.command"
```
## Quick Start
**Automatic Database Setup:**
```python
import os
os.environ["PLANNOTATE_AUTO_DOWNLOAD"] = "1" # Enable auto-download
from plannotate.annotate import annotate
# First run will download databases (~900MB with progress bars)
sequence = "ATGGTGAGCAAGGGCGAGGAGCTG" # Your plasmid sequence
result = annotate(sequence, linear=False) # False for circular plasmids
print(f"Found {len(result)} annotations")
print(result[['Feature', 'Type', 'qstart', 'qend', 'pident']].head())
```
**Manual Database Setup:**
```python
from plannotate.resources import download_db
download_db() # Downloads with progress bars and SSL error handling
```
**Generate GenBank Files:**
```python
from plannotate.resources import get_gbk
gbk_content = get_gbk(result, sequence, is_linear=False)
with open("my_plasmid.gbk", "w") as f:
f.write(gbk_content)
```
## Configuration
**Environment Variables:**
- `PLANNOTATE_AUTO_DOWNLOAD=1` - Auto-download databases without prompting
- `PLANNOTATE_DB_DIR=/path` - Custom database directory
- `PLANNOTATE_SKIP_DB_DOWNLOAD=1` - Skip database downloads entirely
**Core Functions:**
- `annotate(sequence, linear=False)` - Annotate DNA sequence
- `get_gbk(annotations, sequence)` - Generate GenBank file
- `download_db()` - Download databases with progress bars
## Troubleshooting
**SSL Certificate Errors:** Run the SSL certificate fix command above
**Empty Results:** Sequence may not match database features
**Tool Errors:** Ensure external tools are installed and in PATH
## Citation
If you use `pLannotate-python` in your research, please cite the original pLannotate paper:
> McGuffin, M.J., Thiel, M.C., Pineda, D.L. et al. pLannotate: automated annotation of engineered plasmids. *Nucleic Acids Research* (2021).
## License
This project is licensed under the GPL v3 License - see the `LICENSE` file for details.
## Links
- **Original pLannotate**: https://github.com/mmcguffi/pLannotate
- **Web server**: http://plannotate.barricklab.org/
- **This Fork**: https://github.com/McClain-Thiel/pLannotate
- **Issues**: https://github.com/McClain-Thiel/pLannotate/issues
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