RepeatAnalyzer

NOTE: This is a new home for the RepeatAnalyzer project found at: https://bitbucket.org/repeatgroup/repeatanalyzer/src/master/

RepeatAnalyzer is a tool for tracking, managing, analyzing and cataloguing short-sequence repeats and genotypes. It was originally built with model species Anaplasma marginale in mind, but has since been used fro Anaplasma centrale and tested with Streptococcus pneumoniea.

User Setup

Please refer to the user quickstart guide

Dev Setup

Requires: Python 3.10+ poetry Windows or Mac OS (project may work partially in Linux but HAS NOT been tested. Development/testing in Mac OS is limited) Depending on your MacOs version, you may need to install additional dependencies for certain python libraries. see "Install Macos Dependencies" in .github/workflows/build.yml in this project for more details.

Requirements for this project are managed with poetry. That means first time setup should entail only the follwing, assuming your python installation is on the system path. If it is not, you can replace 'python' in the first command below with your desired system python version. Once this is done, you can always run code for this project with poetry run python. A managed virtual environment will be created on your system by poetry. For more information, use poetry --help

    python -m pip install poetry
    poetry install
    poetry run python main.py
    poetry run pre-commit install  # this will activate the hooks in .pre-commit-config.yml

pre-commit

This repository uses pre-commit to automate certain linting and style checks required by the project. For more information, read https://github.com/pre-commit/pre-commit-hooks

Documenting changes

Please include any changes you would like to have merged to the main branch to CHANGELOG.md

Notes

The most up to date version of RepeatAnalyzer.dat that I have been using in testing is also there. It currently only has data for A. marginale and is not complete.

Additionally, some locations are stored incorrectly. For instance, in South Africa, "freestate" will not return any results because the data is stored to "northeastern freestate". There are analogous problems for several areas.

The MapData folder holds shapefiles of the borders used in mapping, collected from naturalearthdata.com

For areas with more than 15 or so repeats on a single point, pie charts will become blurred.

Legends may also run off the map if they contain over 20 or so entries.