Metadata-Version: 2.4
Name: nanotimesort
Version: 1.1.1
Summary: Bin Oxford Nanopore reads by cumulative sequencing time intervals (Guppy and Dorado compatible)
Author-email: Marc-Olivier Duceppe <duceppemo@gmail.com>
License: MIT License
        
        Copyright (c) 2019 Marc-Olivier Duceppe
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/duceppemo/nanoTimeSort
Project-URL: Issues, https://github.com/duceppemo/nanoTimeSort/issues
Project-URL: Wiki, https://github.com/duceppemo/nanoTimeSort/wiki
Keywords: nanopore,fastq,bioinformatics,minion,dorado,guppy,binning
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Dynamic: license-file

<p align="center">
  <img src="docs/images/logo.svg" alt="nanoTimeSort" width="520">
</p>

<p align="center">
  <a href="https://pypi.org/project/nanotimesort/"><img src="https://img.shields.io/pypi/v/nanotimesort.svg" alt="PyPI"></a>
  <a href="https://github.com/duceppemo/nanoTimeSort/actions/workflows/ci.yml"><img src="https://github.com/duceppemo/nanoTimeSort/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
  <a href="https://codecov.io/gh/duceppemo/nanoTimeSort"><img src="https://codecov.io/gh/duceppemo/nanoTimeSort/branch/master/graph/badge.svg" alt="codecov"></a>
  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT"></a>
  <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/python-3.8%2B-blue.svg" alt="Python 3.8+"></a>
  <a href="pyproject.toml"><img src="https://img.shields.io/badge/dependencies-none-brightgreen.svg" alt="No dependencies"></a>
  <a href="https://zenodo.org/badge/latestdoi/209610655"><img src="https://zenodo.org/badge/209610655.svg" alt="DOI"></a>
</p>

Bin Oxford Nanopore reads by **cumulative sequencing time intervals**, using the read start time
that MinKNOW, Guppy and Dorado embed in every FASTQ header. Useful to answer *"how long did I
actually need to sequence?"* — for time-to-detection studies, assembly saturation curves, or
benchmarking real-time pipelines.

```text
fastq_pass/  ──►  sample_0-1h_125437reads_1103093674bp.fastq.gz
                  sample_0-2h_225891reads_2087456221bp.fastq.gz   (bins are cumulative)
                  sample_0-3h_301255reads_2812345678bp.fastq.gz
```

Compatible with **Guppy/MinKNOW** (`start_time=`) and **Dorado** (`st:Z:`) headers. Fast
(each read compressed once, ~100× faster than v0.1), low-memory (streaming), parallel, and
pure standard library.

## Install

```bash
pip install nanotimesort
```

Requires Python ≥ 3.8. No other dependencies.

## Usage

```bash
nanotimesort -f /path/to/fastq_pass/ -o /path/to/output/ -i 1h -p my_sample
```

📖 **Full documentation** — CLI reference, tutorial with example data, header compatibility,
design notes and FAQ — is in the [**wiki**](https://github.com/duceppemo/nanoTimeSort/wiki).

## Citation

If you use nanoTimeSort in your research, please cite it. GitHub's **"Cite this repository"**
button (from [`CITATION.cff`](CITATION.cff)) gives APA/BibTeX entries, and the DOI badge above
resolves to the citable Zenodo archive of the latest release.

## License

[MIT](LICENSE) © Marc-Olivier Duceppe
