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

Last update: Mar 10, 2022

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.

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Comments

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

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

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
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)

0.1.8(Mar 10, 2022)

To support python versions older than 3.9. A better solution for avoiding recomputing irreps etc is incoming!
Source code(tar.gz)
Source code(zip)
0.1.7(Mar 8, 2022)
What's Changed

Bug fixes and small changes for RECOMB-CG paper submission by @js51 in https://github.com/js51/Circular-genome-tools/pull/34

Add support for computing conjugacy classes by @js51 in https://github.com/js51/Circular-genome-tools/pull/36

Full Changelog: https://github.com/js51/Circular-genome-tools/compare/0.1.3...0.1.7
Source code(tar.gz)
Source code(zip)
0.1.5(Aug 20, 2021)

Source code(tar.gz)
Source code(zip)
0.1.3(Jul 9, 2021)

Nothing major, but makes getting likelihood functions easier!
Source code(tar.gz)
Source code(zip)
0.1.1(Jul 1, 2021)

Source code(tar.gz)
Source code(zip)
0.1.0(Jun 25, 2021)

Removes a lot of old code! Won't be compatible with my old scripts any more. Add models and other things. Still a lot more stuff to go in.
Source code(tar.gz)
Source code(zip)
0.0.14(Jun 21, 2021)

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)
Source code(tar.gz)
Source code(zip)
0.0.7(Aug 4, 2020)

Source code(tar.gz)
Source code(zip)
0.0.6(Aug 4, 2020)

Source code(tar.gz)
Source code(zip)
0.0.4(Jul 29, 2020)

Source code(tar.gz)
Source code(zip)
0.0.2(Mar 3, 2020)

Source code(tar.gz)
Source code(zip)

Owner

Joshua Stevenson

PhD Student at the University of Tasmania

GitHub Repository https://cgt.joshuastevenson.me

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

Related tags

Overview

Circular genome tools (cgt)

You might also like...

fetchmesh is a tool to simplify working with Atlas anchoring mesh measurements

Providing a working, flexible, easier and faster installer than the one officially provided by Arch Linux

Service for working with open data of the State Duma of the Russian Federation

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A Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library

Comments

Remove old code, replace most of it.

Rewrite

Make it easier to compute MLEs for multiple genomes

Improve genome visualisation module

Releases(0.1.8)

0.1.8(Mar 10, 2022)

0.1.7(Mar 8, 2022)

What's Changed

0.1.5(Aug 20, 2021)

0.1.3(Jul 9, 2021)

0.1.1(Jul 1, 2021)

0.1.0(Jun 25, 2021)

0.0.14(Jun 21, 2021)

0.0.7(Aug 4, 2020)

0.0.6(Aug 4, 2020)

0.0.4(Jul 29, 2020)

0.0.2(Mar 3, 2020)