A sage package for working with circular genomes represented by signed or unsigned permutations

Related tags

Miscellaneouspythonbioinformaticsmathematicssagegappermutationssagemathgenome-rearrangmentsigned-permutationcircular-genomeutascircular-genomessagemath9
Overview

Circular genome tools (cgt)

A sage package for working with circular genomes represented by signed or unsigned permutations. It includes tools for converting between representations as well as visualisations using matplotlib.

To install and use this package, paste the following command in your terminal

sage -pip install cgt

and use import cgt in a sage script or environment.

If you would like to contribute to cgt, please see CONTRIBUTING.md for how to get set up.

If you use this software in your work, please cite it use the citation function on the github page or see CITATION.cff

Note: you will need to at least have Sage version 9.0 installed, and have the GAP package repsn installed for the copy of GAP that sits inside Sage. If you aren't sure how to do this, see the installation instructions in INSTALL.md.

You might also like...
fetchmesh is a tool to simplify working with Atlas anchoring mesh measurements
fetchmesh is a tool to simplify working with Atlas anchoring mesh measurements

A Python library for working with the RIPE Atlas anchoring mesh. fetchmesh is a tool to simplify working with Atlas anchoring mesh measurements. It ca

null 2 Aug 30, 2022
Providing a working, flexible, easier and faster installer than the one officially provided by Arch Linux
Providing a working, flexible, easier and faster installer than the one officially provided by Arch Linux

Purpose The purpose is to bring more people to Arch Linux by providing a working, flexible, easier and faster installer than the one officially provid

André Luís 0 Nov 9, 2022
Service for working with open data of the State Duma of the Russian Federation
Service for working with open data of the State Duma of the Russian Federation

Сервис для работы с открытыми данными Госдумы РФ Исходные данные из API Госдумы РФ извлекаются с помощью Apache Nifi и приземляются в хранилище Clickh

Aleksandr Sergeenko 2 Feb 14, 2022
Tool for working with Direct System Calls in Cobalt Strike's Beacon Object Files (BOF) via Syswhispers2

Tool for working with Direct System Calls in Cobalt Strike's Beacon Object Files (BOF) via Syswhispers2

null 150 Dec 31, 2022
A wrapper script to make working with ADB (Android Debug Bridge) easier

Python-ADB-Wrapper A wrapper script to make working with ADB (Android Debug Bridge) easier This project was just a simple test to see if I could wrap

18iteration 1 Nov 25, 2021
A working roblox account generator it doesnt bypass the capcha stuff cuz these didnt showed up in my test runs
A working roblox account generator it doesnt bypass the capcha stuff cuz these didnt showed up in my test runs

A working roblox account generator (state 11.5.2021) it doesnt bypass the capcha stuff cuz these didnt showed up in my test runs

TerrificTable 22 Jan 3, 2023
Simple project to assist in tracking/logging my working hours

Fill working hours Basic script to assist in the logging/tracking of my working hours How it works Create a file called projects.json in this director

Robin Kennedy-Reid 2 Oct 31, 2022
NASH 2021 project... this may or may not end up working 🤷‍♂️

wavespace synthesiser this is my NASH 2021 project, which may or may not end up working 🤷‍♂️ what is going on? imagine you have a big folder of audio

Ben Hayes 12 May 17, 2022
A Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library

gdsclient NOTE: This is a work in progress and many GDS features are known to be missing or not working properly. This repo hosts the sources for gdsc

Neo4j 100 Dec 20, 2022
Comments
  • Remove old code, replace most of it.

    Remove old code, replace most of it.

    From this point on the package is no longer compatible with my old scripts, but the interface is hopefully much nicer. Will merge into main once all the functionality is back.

    opened by js51 0
  • Rewrite

    Rewrite

    Haven't deleted anything so should still be backwards compatible with old code. The major change is the new PositionParadigmFramework class which consolidates a lot of information so it doesn't need to be passed around to do simple things. Should be a lot easier to use and to test.

    The long term goal is to move everything into the PositionParadigmFramework class, or make new classes with functions that accept a PositionParadigmFramework instance. Also started a Genome class which will allow a nicer syntax, printing etc for dealing with entire genomes (as cosets of permutations)

    opened by js51 0
  • Make it easier to compute MLEs for multiple genomes

    Make it easier to compute MLEs for multiple genomes

    the irreps, eigenvalues, projections etc are currently recomputed every time. Caching won't work because they aren't hashable but we should be able to store them in memory some other way, or allow the user to pass them around.

    opened by js51 0
  • Improve genome visualisation module

    Improve genome visualisation module

    This was thrown together quite quickly and could do with some improvements:

    • [ ] More options for representing genomes (currently they need to be converted to a position paradigm (reg->pos) list
    • [ ] Option to save image files with transparency
    • [ ] Option to move arrows to the ends of each region
    • [ ] Option to have a gap instead of a line separating regions
    • [ ] TikZ output (probably a complete rewrite)
    • [ ] Option to change output size
    • [ ] Label sizing options
    • [ ] #31
    enhancement help wanted 
    opened by js51 1
Releases(0.1.8)
Owner
Joshua Stevenson
PhD Student at the University of Tasmania
Joshua Stevenson
GitHub Repository https://cgt.joshuastevenson.me
An early stage integration of Hotwire Turbo with Django

Note: This is not ready for production. APIs likely to change dramatically. Please drop by our Slack channel to discuss!

Hotwire for Django 352 Jan 06, 2023
A Python 3 client for the beanstalkd work queue

Greenstalk Greenstalk is a small and unopinionated Python client library for communicating with the beanstalkd work queue. The API provided mostly map

Justin Mayhew 67 Dec 08, 2022
This package tries to emulate the behaviour of syntax proposed in PEP 671 via a decorator

Late-Bound Arguments This package tries to emulate the behaviour of syntax proposed in PEP 671 via a decorator. Usage Mention the names of the argumen

Shakya Majumdar 0 Feb 06, 2022
A program that analyzes data from inertia measurement units installeed in aircraft and generates g-exceedance curves

A program that analyzes data from inertia measurement units installeed in aircraft and generates g-exceedance curves

Pooya 1 Nov 23, 2021
Collection of functions for working with interlaced content in VapourSynth.

vsfieldkit Collection of functions for working with interlaced content in VapourSynth. It does not have any hard dependencies outside of VapourSynth.

Justin Turner Arthur 11 May 27, 2022
A web app that is written entirely in Python

University Project About I made this web app to finish a project assigned by my teacher. It is written entirely in Python, thanks to streamlit to make

15 Nov 27, 2022
contextlib2 is a backport of the standard library's contextlib module to earlier Python versions.

contextlib2 is a backport of the standard library's contextlib module to earlier Python versions. It also sometimes serves as a real world proving gro

Jazzband 35 Dec 23, 2022
News-app - This is a news web app for reading news from different sources and topics

News-app - This is a news web app for reading news from different sources and topics

1 Feb 02, 2022
Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. 💛💙💚

Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. 💛💙💚

Raja Rakotonirina 2 Jan 10, 2022
A Dungeon and Dragons Toolkit using Python

Pythons-Dungeons A Dungeon and Dragons Toolkit using Python Rules: -When you are commiting please don't delete parts of the code that are important -A

2 Oct 21, 2021
Similarity checking of sign languages

Similarity checking of sign languages This repository checks for similarity betw

Tonni Das Jui 1 May 13, 2022
This is a far more in-depth and advanced version of "Write user interface to a file API Sample"

Fusion360-Write-UserInterface This is a far more in-depth and advanced version of "Write user interface to a file API Sample" from https://help.autode

4 Mar 18, 2022
Fused multiply-add (with a single rounding) for Python.

pyfma Fused multiply-add for Python. Fused multiply-add computes (x*y) + z with a single rounding. Useful for dot products, matrix multiplications, po

Nico Schlömer 18 Nov 08, 2022
A synchronous, single-threaded interface for starting processes on Linux

A synchronous, single-threaded interface for starting processes on Linux

Spencer Baugh 27 Jan 28, 2022
Basit bir sunucu - istemci örneği

basitSunucuistemci Aşağıdaki adresteki uygulamadaki process kapanmama sorununun çözülmesi ile oluşturulmuş yeni depo https://github.com/pricheal/pytho

Ali Orhun Akkirman 10 Dec 27, 2022
A Trace Explorer for Reverse Engineers

Tenet - A Trace Explorer for Reverse Engineers Overview Tenet is an IDA Pro plugin for exploring execution traces. The goal of this plugin is to provi

1k Jan 02, 2023
Osu statistics right on your desktop, made with pyqt

Osu!Stat Osu statistics right on your desktop, made with Qt5 Credits Would like to thank these creators for their projects and contributions. ppy, osu

Aditya Gupta 21 Jul 13, 2022
Library management using python & MySQL

Library management using python & MySQL Dev/Editor: Pavan Ananth Sharma & MK Akash Introduction: This is an intermediate project which is a user-frie

Pavan Ananth Sharma 2 Jul 05, 2022
Painel simples com consulta de cep,CNPJ,placa e ip

Painel mpm Um painel simples com consultas de IP, CNPJ, CEP, PLACA, TELEFONE, CPF e NOME Início 🌐 apt update && apt upgrade -y pkg i python git pip i

8 Feb 27, 2022
Reference python implementation of Chia pool operations for pool operators

This repository provides a sample server written in python, which is meant to server as a basis for a Chia Pool. While this is a fully functional implementation, it requires some work in scalability

Chia Network 451 Dec 13, 2022