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image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10548864.svg\n  :target: https://doi.org/10.5281/zenodo.10548864\n\n.. image:: https://github.com/marcelm/dnaio/workflows/CI/badge.svg\n    :alt: GitHub Actions badge\n\n.. image:: https://img.shields.io/pypi/v/dnaio.svg?branch=main\n    :target: https://pypi.python.org/pypi/dnaio\n    :alt: PyPI badge\n\n.. image:: https://codecov.io/gh/marcelm/dnaio/branch/master/graph/badge.svg\n    :target: https://codecov.io/gh/marcelm/dnaio\n    :alt: Codecov badge\n\n===========================================\ndnaio processes FASTQ, FASTA and uBAM files\n===========================================\n\n``dnaio`` is a Python 3.9+ library for very efficient parsing and writing of FASTQ and also FASTA files.\nSince ``dnaio`` version 1.1.0, support for efficiently parsing uBAM files has been implemented.\nThis allows reading ONT files from the `dorado \u003chttps://github.com/nanoporetech/dorado\u003e`_\nbasecaller directly.\n\nThe code was previously part of the\n`Cutadapt \u003chttps://cutadapt.readthedocs.io/\u003e`_ tool and has been improved significantly since it has been split out.\n\nExample usage\n=============\n\nThe main interface is the `dnaio.open \u003chttps://dnaio.readthedocs.io/en/latest/api.html\u003e`_ function::\n\n    import dnaio\n\n    with dnaio.open(\"reads.fastq.gz\") as f:\n        bp = 0\n        for record in f:\n            bp += len(record)\n    print(f\"The input file contains {bp/1E6:.1f} Mbp\")\n\nFor more, see the `tutorial \u003chttps://dnaio.readthedocs.io/en/latest/tutorial.html\u003e`_ and\n`API documentation \u003chttps://dnaio.readthedocs.io/en/latest/api.html\u003e`_.\n\nInstallation\n============\n\nUsing pip::\n\n    pip install dnaio zstandard\n\n``zstandard`` can be omitted if support for Zstandard (``.zst``) files is not required.\n\nFeatures and supported file types\n=================================\n\n- FASTQ input and output\n- FASTA input and output\n- BAM input\n- Compressed input and output (``.gz``, ``.bz2``, ``.xz`` and ``.zst`` are detected automatically)\n- Paired-end data in two files\n- Interleaved paired-end data in a single file\n- Files with DOS/Windows linebreaks can be read\n- FASTQ files with a second header line (after the ``+``) are supported\n\nLimitations\n===========\n\n- Multi-line FASTQ files are not supported\n- FASTQ and uBAM parsing is the focus of this library. The FASTA parser is not as optimized\n\nLinks\n=====\n\n* `Documentation \u003chttps://dnaio.readthedocs.io/\u003e`_\n* `Source code \u003chttps://github.com/marcelm/dnaio/\u003e`_\n* `Report an issue \u003chttps://github.com/marcelm/dnaio/issues\u003e`_\n* `Project page on PyPI \u003chttps://pypi.python.org/pypi/dnaio/\u003e`_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcelm%2Fdnaio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarcelm%2Fdnaio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcelm%2Fdnaio/lists"}