Metadata-Version: 2.1
Name: dnaio
Version: 0.4.1
Summary: Read FASTA and FASTQ files efficiently
Home-page: https://github.com/marcelm/dnaio/
Author: Marcel Martin
Author-email: marcel.martin@scilifelab.se
License: MIT
Description: [![Travis](https://travis-ci.org/marcelm/dnaio.svg?branch=master)](https://travis-ci.org/marcelm/dnaio)
        [![PyPI](https://img.shields.io/pypi/v/dnaio.svg?branch=master)](https://pypi.python.org/pypi/dnaio)
        [![Codecov](https://codecov.io/gh/marcelm/dnaio/branch/master/graph/badge.svg)](https://codecov.io/gh/marcelm/dnaio)
        
        # dnaio parses FASTQ and FASTA
        
        `dnaio` is a Python 3 library for fast parsing of FASTQ and also FASTA files. The code was previously part of the
        [Cutadapt](https://cutadapt.readthedocs.io/) tool and has been improved 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')
        
        
        ## Features and supported file types
        
        - FASTQ input and output
        - FASTA input and output
        - Compressed input and output (`.gz`, `.bz2` and `.xz`, 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. You shouldn’t use them anyway.
        - FASTQ parsing is the focus of this library. The FASTA parser is not as optimized.
        
        
        # Links
        
        * [Source code](https://github.com/marcelm/dnaio/)
        * [Report an issue](https://github.com/marcelm/dnaio/issues)
        * [Project page on PyPI](https://pypi.python.org/pypi/dnaio/)
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.4
Description-Content-Type: text/markdown
Provides-Extra: dev