dnaio 0.4.1

Read FASTA and FASTQ files efficiently

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 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
• Report an issue
• Project page on PyPI