GithubHelp home page GithubHelp logo

codon_degeneracy's Introduction

Codon Degeneracy

This script 0-fold 2-fold and 4-fold codon degeneracy sites from a genome. It requires a genome fasta file and a gff file.

Getting Started

Prerequisites

Python3

Installing

Download the python script

Command line

python3 degeneracy myannotation.gff3 mygenome.fastas

The output are three files: deglist_0fold_sorted.bed deglist_2fold_sorted.bed deglist_4fold_sorted.bed

The position in the bed file conforms to bed file standard (0 based in the 2nd column, 1 based in the 3rd column), and it is the position of the mutable nucleotide not the codon start. The Name column of the bed file includes the following field: type, transcript ID, codon position in the CDS (0 based), codon position in the chromosome (0 based), mutation postion offset from codon start, codon

Authors

  • Qi Sun - Initial work

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

codon_degeneracy's People

Contributors

qisun2 avatar

Watchers

 avatar

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.