dnaio

Efficiently read and write sequencing data from Python

https://github.com/marcelm/dnaio

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Efficiently read and write sequencing data from Python

README.rst

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===========================================
dnaio processes FASTQ, FASTA and uBAM files
===========================================

``dnaio`` is a Python 3.9+ library for very efficient parsing and writing of FASTQ and also FASTA files.
Since ``dnaio`` version 1.1.0, support for efficiently parsing uBAM files has been implemented.
This allows reading ONT files from the `dorado `_
basecaller directly.

The code was previously part of the
`Cutadapt `_ tool and has been improved significantly since it has been split out.

Example usage
=============

The main interface is the `dnaio.open `_ function::

    import dnaio

    with dnaio.open("reads.fastq.gz") as f:
        bp = 0
        for record in f:
            bp += len(record)
    print(f"The input file contains {bp/1E6:.1f} Mbp")

For more, see the `tutorial `_ and
`API documentation `_.

Installation
============

Using pip::

    pip install dnaio zstandard

``zstandard`` can be omitted if support for Zstandard (``.zst``) files is not required.

Features and supported file types
=================================

- FASTQ input and output
- FASTA input and output
- BAM input
- Compressed input and output (``.gz``, ``.bz2``, ``.xz`` and ``.zst`` are detected automatically)
- Paired-end data in two files
- Interleaved paired-end data in a single file
- Files with DOS/Windows linebreaks can be read
- FASTQ files with a second header line (after the ``+``) are supported

Limitations
===========

- Multi-line FASTQ files are not supported
- FASTQ and uBAM parsing is the focus of this library. The FASTA parser is not as optimized

Links
=====

* `Documentation `_
* `Source code `_
* `Report an issue `_
* `Project page on PyPI `_

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
title: dnaio
type: software
authors:
  - given-names: Marcel
    family-names: Martin
    orcid: 'https://orcid.org/0000-0002-0680-200X'
  - given-names: Ruben Harmen Paul
    family-names: Vorderman
    orcid: 'https://orcid.org/0000-0002-8813-1528'
identifiers:
  - type: doi
    value: 10.5281/zenodo.10548864
repository-code: 'https://github.com/marcelm/dnaio/'
url: 'https://dnaio.readthedocs.io/'
license: MIT

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