KMTools

Bits of reusable code to make our lives easier.

Follows the Whole Sort of General Mish Mash design principle.

Contents

• Tools
  • DB tools
  • DF tools
  • PY tools
  • Sequence tools
  • Structure tools
  • System tools
• Contributing

Tools

Structure tools

Using kmbio instead of 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.