heyfastq 0.1.0

FASTQ utilities

heyfastq

FASTQ sequence file utilities, written in pure Python, with no dependencies.

Summary

The package comes with one program, heyfastq, which provides utilities for single or paired FASTQ files.

Installation

Install from PyPi with:

pip install heyfastq

Or get the dev version from GitHub:

git clone https://github.com/kylebittinger/heyfastq.git
pip install .

Usage

Run heyfastq -h to learn more about usage options.

As dependency

To include heyfastqlib in your own Python code, include it as a dependency (only available via GH atm). Then import the objects/functions you need and enjoy your fastqs.

e.g. your very own wrapper for fastq_parse that only returns the sequences

import gzip
from heyfastqlib.io import parse_fastq
from typing import Generator

def fastq_reads(path: str) -> Generator[str, None, None]:
    with gzip.open("/path/to/my_file_R1.fastq.gz", "rt") as f:
        return (read.seq for read in parse_fastq(f.readlines()))