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Bits of reusable code to make our lives easier.

Project description

# KMTools

[![anaconda](https://img.shields.io/conda/dn/kimlab/kmtools.svg)](https://anaconda.org/kimlab/kmtools/) [![docs](https://img.shields.io/badge/docs-v0.0.27-blue.svg?version=latest)](https://kimlab.gitlab.io/kmtools/v0.0.27/) [![build status](https://gitlab.com/kimlab/kmtools/badges/v0.0.27/build.svg)](https://gitlab.com/kimlab/kmtools/commits/v0.0.27/) [![coverage report](https://gitlab.com/kimlab/kmtools/badges/v0.0.27/coverage.svg)](https://kimlab.gitlab.io/kmtools/v0.0.27/htmlcov/)

Bits of reusable code to make our lives easier.

Follows the Whole Sort of General Mish Mash design principle.

## Contents

  • [Tools](#tools) - [DB tools](#db-tools) - [DF tools](#df-tools) - [PY tools](#py-tools) - [Sequence tools](#sequence-tools) - [Structure tools](#structure-tools) - [System tools](#system-tools)
  • [Contributing](#contributing)

## Tools

### Structure tools

Using [kmbio](https://github.com/kimlaborg/kmbio) instead of [biopython](https://github.com/biopython/biopython) leads to substantially better performance (> 2x with lots of room for improvement).

#### To do

  • [ ] Cythonize more bottlenecks to improve performance.
  • [ ] Add Python / Cython code for generating biological assemblies.

## Contributing

  • Make sure all tests pass before merging into master.
  • Follow the PEP8 / PyFlake / Flake8 / etc. guidelines.
  • Add tests for new code.
  • Try to document things.
  • Break any / all of the above if you have a good reason.

Project details


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