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
AIO solution for SSIS students

ssis.bit AIO solution for SSIS students Hardware CircuitPython supports more than 200 different boards. Locally available is the TTGO T8 ESP32-S2 ST77

3 Jun 05, 2022
IPython: Productive Interactive Computing

IPython: Productive Interactive Computing Overview Welcome to IPython. Our full documentation is available on ipython.readthedocs.io and contains info

IPython 15.6k Dec 31, 2022
Alternative StdLib for Nim for Python targets

Alternative StdLib for Nim for Python targets, hijacks Python StdLib for Nim

Juan Carlos 100 Jan 01, 2023
A fishing bot script written in Python!

A fishing bot script written in Python!

Anel Drocic 3 Nov 03, 2021
An Android app that runs Elm in a webview. And a Python script to build the app or install it on the device.

Requirements You need to have installed: the Android SDK Elm Python git Starting a project Clone this repo and cd into it: $ git clone https://github.

Benjamin Le Forestier 11 Mar 17, 2022
Nextstrain build targeted to Omicron

About This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, e

Bedford Lab 9 May 25, 2022
A Python Web Application for Checking vaccine slots by pincodes and auto slot booking.

The Dashboard is developed using Bokeh and python 3.5+. This dashboard is useful for you if you are looking for something which will help you to book the vaccine slot once slots become available. Oth

Suraj Deshmukh 10 Jan 23, 2022
Mmr image postbot - Бот для создания изображений с новыми релизами в сообщество ВК MMR Aggregator

Mmr image postbot - Бот для создания изображений с новыми релизами в сообщество ВК MMR Aggregator

Max 3 Jan 07, 2022
When should you berserk in lichess arena tournament games?

When should you berserk in a lichess arena tournament game? 1+0 arena tournament 3+0 arena tournament Explanation For details on how I arrived at the

18 Aug 03, 2022
Python calculator made with tkinter package

Python-Calculator Python calculator made with tkinter package. works both on Visual Studio Code Or Any Other Ide Or You Just Copy paste The Same Thing

Pro_Gamer_711 1 Nov 11, 2021
Open HW & SW for Scanning Electron Microscopes

OpenSEM Project Status: Preliminary The purpose of this project is to create a modern and open-source hardware and software platform for using vintage

Steven Lovegrove 7 Nov 01, 2022
A student information management system in Python

Student-information-management-system 本项目是一个学生信息管理系统，这个项目是用Python语言实现的，也实现了图形化界面的显示，同时也实现了管理员端，学生端两个登陆入口，同时底层使用的是Redis做的数据持久化。 This project is a stude

liuyunfei 7 Nov 15, 2022
A prototype COG-based tile server for sparse Mars datasets

Mars tiler Mars Tiler is a prototype web application that serves tiles from cloud-optimized GeoTIFFs, with an emphasis on supporting planetary dataset

Daven Quinn 3 Mar 23, 2022
A webapp that timestamps key moments in a football clip

A look into what we're building Demo.mp4 Prerequisites Python 3 Node v16+ Steps to run Create a virtual environment. Activate the virtual environment.

Pranav 1 Dec 10, 2021
Basic Hspice runner with Python

HSpicePy Bilgisayarınıza PATH değişkenlerine eklediğiniz HSPICE programını python ile çalıştırmanızı sağlayan basit bir araç. A simple tool that allow

1 Nov 16, 2021
Scientific Programming: A Crash Course

Scientific Programming: A Crash Course Welcome to the Scientific Programming course. My name is Jon Carr and I am a postdoc in Davide Crepaldi's lab.

Jon Carr 1 Feb 17, 2022
PhD document for navlab

PhD_document_for_navlab The project contains the relative software documents which I developped or used during my PhD period. It includes: FLVIS. A st

ZOU YAJING 9 Feb 21, 2022
A Python module for decorators, wrappers and monkey patching.

wrapt The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function

Graham Dumpleton 1.8k Jan 06, 2023
PyPI package for scaffolding out code for decision tree models that can learn to find relationships between the attributes of an object.

Decision Tree Writer This package allows you to train a binary classification decision tree on a list of labeled dictionaries or class instances, and

2 Apr 23, 2022
Pytorch implementation of "Peer Loss Functions: Learning from Noisy Labels without Knowing Noise Rates"

Peer Loss functions This repository is the (Multi-Class & Deep Learning) Pytorch implementation of "Peer Loss Functions: Learning from Noisy Labels wi

Kushal Shingote 1 Feb 08, 2022