Operon

test status codecov

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.

Project links

Data verified by PyPI on Sep 12, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for hyli360 from gravatar.com hyli360

Credits

Author: hyli360

GitHub Statistics

Data verified by PyPI on Sep 12, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

AGPL-3.0-or-later
View SPDX License List

Requires

Python >=3.10

Provides Extra

test docs dev

Classifiers

Report project as malware

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This release

0.8.0 This release

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0.6.2

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