Giter VIP home page Giter VIP logo

nthash's Introduction

ntHash

ntHash implementation in Go


travis GoDoc goreportcard codecov

Overview

This is a Go implementation of the ntHash recursive hash function for hashing all possible k-mers in a DNA/RNA sequence.

For more information, read the ntHash paper by Mohamadi et al. or check out their C++ implementation.

This implementation was inspired by Luiz Irber and his recent blog post on his cool Rust ntHash implementation.

I have coded this up in Go so that ntHash can be used in my HULK and GROOT projects but feel free to use it for yourselves.

Installation

go get github.com/will-rowe/nthash

Example usage

range over ntHash values for a sequence

package main

import (
    "log"
    "github.com/will-rowe/nthash"
)

var (
    sequence = []byte("ACGTCGTCAGTCGATGCAGTACGTCGTCAGTCGATGCAGT")
    kmerSize = 11
)

func main() {

    // create the ntHash iterator using a pointer to the sequence and a k-mer size
    hasher, err := ntHash.New(&sequence, kmerSize)

    // check for errors (e.g. bad k-mer size choice)
    if err != nil {
        log.Fatal(err)
    }

    // collect the hashes by ranging over the hash channel produced by the Hash method
    canonical := true
    for hash := range hasher.Hash(canonical) {
        log.Println(hash)
    }
}

nthash's People

Contributors

shenwei356 avatar will-rowe avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar

nthash's Issues

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.