Operon

A Python-based, file-based database designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.

点此阅读中文自述文件。

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_by allows thresholds to be selected based on classification metrics such as BUSCO auto-lineage
Encapsulated External Analysis: config/tools.yaml specifies the launch methods for BLAST/HMMER/BUSCO, artifact types, constrained runtime parameters, version detection, caching, and result write-back; analyze executes 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-qc can 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, and questionary; the built-in QC acceleration extension is compiled when the package is built
Optional extras: test (pytest and Cython), docs (documentation tooling), and dev (all development/build dependencies)

Install

# Install the published package
python3 -m venv .venv
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. To build the Sphinx site locally:

python -m pip install -e '.[docs]'
sphinx-build -W --keep-going -b html docs docs/_build/html

Read the Docs uses the repository's .readthedocs.yaml configuration and publishes a language-selection page with mirrored /en/ and /zh/ documentation trees.

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OperonDBS 0.7.2

Operon

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