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
Beacon Object File (BOF) to obtain a usable TGT for the current user.

Beacon Object File (BOF) to obtain a usable TGT for the current user.

Connor McGarr 109 Dec 25, 2022
Static bytecode simulator

SEA Static bytecode simulator for creating dependency/dependant based experimental bytecode format for CPython. Example a = random() if a = 5.0:

Batuhan Taskaya 23 Jun 10, 2022
It is a Blender Tool which can convert the Object Data Attributes in face corner to the UVs or Vertex Color.

Blender_ObjectDataAttributesConvertTool It is a Blender Tool which can convert the Object Data Attributes in face corner to the UVs or Vertex Color. D

Takeshi Chō 2 Jan 08, 2022
A repository containing an introduction to Panel made to be support videos and talks.

👍 Awesome Panel - Introduction to Panel THIS REPO IS WORK IN PROGRESS. PRE-ALPHA Panel is a very powerful framework for exploratory data analysis and

Marc Skov Madsen 51 Nov 17, 2022
Performance data for WASM SIMD instructions.

WASM SIMD Data This repository contains code and data which can be used to generate a JSON file containing information about the WASM SIMD proposal. F

Evan Nemerson 5 Jul 24, 2022
Poetry workspace plugin for Python monorepos.

poetry-workspace-plugin Poetry workspace plugin for Python monorepos. Inspired by Yarn Workspaces. Adds a new subcommand group, poetry workspace, whic

Jack Smith 74 Jan 01, 2023
Feapder的管道扩展

FEAPDER 管道扩展 简介 此模块为feapder的pipelines扩展，感谢广大开发者对feapder的贡献 随着feapder支持的pipelines越来越多，为减少feapder的体积，特将pipelines提出，使用者可按需安装 管道 PostgreSQL 贡献者：沈瑞祥 联系方式：r

boris 9 Dec 07, 2022
Check a discord message and give it a percentage of scamminess

scamChecker Check a discord message and give it a percentage of scamminess Run the bot, and run the command !scamCheck and it will return a percentage

3 Sep 22, 2022
Svg-turtle - Use the Python turtle to write SVG files

SaVaGe Turtle Use the Python turtle to write SVG files If you're using the Pytho

Don Kirkby 7 Dec 21, 2022
Digdata presented 'BrandX' as a clothing brand that wants to know the best places to set up a 'pop up' store.

Digdata presented 'BrandX' as a clothing brand that wants to know the best places to set up a 'pop up' store. I used the dataset given to write a program that ranks these places.

Mahmoud 1 Dec 11, 2021
💘 Write any Python with 9 Characters: e,x,c,h,r,(,+,1,)

💘 PyFuck exchr(+1) PyFuck is a strange playful code. It uses only nine different characters to write Python3 code. Inspired by aemkei/jsfuck Example

Satoki 10 Dec 25, 2022
Generate Azure Blob Storage account authentication headers for Munki

Azure Blob Storage Authentication for Munki The Azure Blob Storage Middleware allows munki clients to connect securely, and directly to a munki repo h

Oliver Kieselbach 10 Apr 12, 2022
Python Programmma DarkMap.py

DarkMap Python Programmma DarkMap.py O'rganish va rasmlarni ko'riosh https://drive.google.com/drive/folders/1l1zybs_0Zy9z_trZYz5R72WrwsE6mFOh?usp=shar

Og'abek 0 May 06, 2022
GDSC UIET KUK 📍 , welcomes you all to this amazing event where you will be introduced to the world of coding 💻 .

GDSC UIET KUK 📍 , welcomes you all to this amazing event where you will be introduced to the world of coding 💻 .

Google Developer Student Club UIET KUK 9 Mar 24, 2022
Check COVID locations of interest against Google location history

Location of Interest Checker Script to compare COVID locations of interest to Google location history. The script produces a map plot (as shown below)

9 Mar 30, 2022
RFDesign - Protein hallucination and inpainting with RoseTTAFold

RFDesign: Protein hallucination and inpainting with RoseTTAFold Jue Wang (juewan

139 Jan 06, 2023
Nimbus - Open Source Cloud Computing Software - 100% Apache2 licensed

⚠️ The Nimbus infrastructure project is no longer under development. ⚠️ For more information, please read the news announcement. If you are interested

Nimbus 194 Jun 30, 2022
Python script to preprocess images of all Pokémon to finetune ruDALL-E

ai-generated-pokemon-rudalle Python script to preprocess images of all Pokémon (the "official artwork" of each Pokémon via PokéAPI) into a format such

Max Woolf 132 Dec 11, 2022
LiteX-Acorn-Baseboard is a baseboard developed around the SQRL's Acorn board (or Nite/LiteFury) expanding their possibilities

LiteX-Acorn-Baseboard is a baseboard developed around the SQRL's Acorn board (or Nite/LiteFury) expanding their possibilities

33 Nov 26, 2022
Tools for dos (denial-of-service) website / web server

DoS Attack Tools Tools for dos (denial-of-service) website / web server di buat olah NurvySec How to install on debian / ubuntu $ apt update $ apt ins

nurvy 1 Feb 10, 2022