Operon the Database System
A Python-based, file-based database designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
Features
- File-based: A single SQLite file (
operon.sqlite) serves as the sole writable source of truth; CSV/XLSX are used for controlled imports, TSV reports are used for read-only exchange, and field contracts are defined by a YAML schema - NCBI Datasets Adapter: Offline-first import of JSON/JSONL, ZIP, or unpacked directories; also supports online download of genome packages with automatic archiving
- Frozen NCBI Taxonomy Coverage: Versioned YAML profiles are compiled into family/genus denominators with SHA-256 hashes, allowing separate auditing of current metadata and immutable releases, and generating a list of missing samples
- Streaming Parsing and Built-in QC: FASTA, FASTQ, GFF3, and protein FASTA files are not loaded entirely into memory; metrics are written to a long table, and decisions are delegated to the versioned YAML profile rule engine;
value_byallows thresholds to be selected based on classification metrics such as BUSCO auto-lineage - Encapsulated External Analysis:
config/tools.yamlspecifies the launch methods for BLAST/HMMER/BUSCO, artifact types, constrained runtime parameters, version detection, caching, and result write-back;analyzeexecutes the entire library or specified categories with a single command - Local Control, Remote Storage and Computing: SQLite, configuration, and provenance are retained locally, while raw large files can reside on a verified SFTP mirror; the execution backend supports local, Slurm, SSH, and remote Slurm environments
- Universal Executor: The structured command executor and
import-qccan integrate with any external tools, such as QUAST, FastQC, fastp, and CheckM2 - Immutable release: Dataset snapshots with manifests, checksums, exclusion reports, and provenance; verifiable via
sha256sum -c
Dependencies
- Python 3.10+
- Runtime dependencies:
PyYAML,requests,aiohttp,Biopython,Paramiko,Textual, andquestionary; the built-in QC acceleration extension is compiled when the package is built - Optional extras:
test(pytest and Cython),docs(documentation tooling), anddev(all development/build dependencies)
Install
For production
We recommend install operon by pipx or uvx.
pipx install operon
# or
uvx install operon
To upgrade, use pipx upgrade operon/uvx upgrade operon.
Install from source code
git clone https://github.com/HYLi360/Operon.git
cd Operon
python3 -m venv .venv # Py 3.10-3.15 are acceptable
source .venv/bin/activate
python -m pip install OperonDBS
For an editable checkout, run from the repository root:
python -m pip install -e '.[dev]'
Documentation
The complete documentation is maintained in English and Chinese. Each language is its own Sphinx project; build both without warnings:
python -m pip install -e '.[docs]'
sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
Read the Docs publishes two projects linked as parent and translation: operonproject (English, https://operonproject.readthedocs.io/en/latest/) and operonproject-zh (Chinese, https://operonproject.readthedocs.io/zh-cn/latest/), each built from its own docs/<language>/.readthedocs.yaml.
1 maintainer
Metadata
1 maintainer
Release files for OperonDBS 0.10.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| operondbs-0.10.2.tar.gz | 1.8 MB | With provenance | Details for operondbs-0.10.2.tar.gz |
Built distributions (wheels)
Total release size: 27.5 MB
Release files / operondbs-0.10.2.tar.gz
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| Tags | Source |
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SHA-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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Transparency logRelease files / operondbs-0.10.2-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | operondbs-0.10.2-cp310-cp310-macosx_10_9_x86_64.whl |
|---|---|
| Size | 986.4 kB |
| Tags | CPython 3.10 macOS 10.9+ x86-64 |
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SHA-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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Transparency logSecurity for OperonDBS 0.10.2
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