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

Related tags

Miscellaneous python bioinformatics mathematics sage gap permutations sagemath genome-rearrangment signed-permutation circular-genome utas circular-genomes sagemath9
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.

    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 https://cgt.joshuastevenson.me
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