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.

Dev

Heyfastq is built around the idea of piping reads (or read pairs) through filter and map functions. The fundamental unit that moves through heyfastq pipelines is the R object, which can be either a Read or a ReadPair. These generic Rs move through functions that take in ReadPipes and output ReadPipes, allowing for easy composition of pipelines.

from heyfastqlib.read import Read, ReadPair, R, ReadPipe
from heyfastqlib.pipelines import filter_reads, map_reads

def unit_filter(r: R) -> bool:
  return True

def unit_map(r: R) -> R:
  return r

input_fastq = (r for r in [Read("1", "ACTG", "HHHH"), Read("2", "GTCA", "HHHH"), Read("3", "AAAA", "####")])
filter_counter = {"input_reads": 0, "input_bases": 0, "output_reads": 0, "output_bases": 0}
map_counter = {"input_reads": 0, "input_bases": 0, "output_reads": 0, "output_bases": 0}

output_fastq = map_reads(filter_reads(input_fastq, unit_filter, filter_counter), unit_map, map_counter)

This is all well and good, but how do we actually deal with fastq files, not just objects already in python?

from heyfastqlib.io import parse_fastq, write_fastq

with open("r1.fq") as f_in, open("o1.fq", "w") as f_out:
  write_fastq(f_out, parse_fastq(f_in))

with open("r1.fq") as f1_in, open("r2.fq") as f2_in, open("o1.fq", "w") as f1_out, open("o2.fq", "w") as f2_out:
  write_fastq((f1_out, f2_out), parse_fastq((f1_in, f2_in)))

Putting it all together, assuming we've imported/created the objects from above, let's read our fastqs then apply our filter then our map and finally write them to fastqs again:

with open("r1.fq") as f1_in, open("r2.fq") as f2_in, open("o1.fq", "w") as f1_out, open("o2.fq", "w") as f2_out:
  write_fastq((f1_out, f2_out), map_reads(filter_reads(parse_fastq((f1_in, f2_in)), unit_filter, filter_counter), unit_map, map_counter))