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Fcup ABI

Python Module for biological sequence handling developed in the course: Algorithms for Bionformatics

Build Status Coverage Status

  • The 1st delivery report can be found here.
  • The 2nd delivery report can be found here.
  • The 3rd delivery report can be found here.

Install

pip install git+https://github.com/msramalho/fcup-abi

Import

To use it simply do import bioseq or from bioseq import DNASeq (for instance).

Demo

You can run any of the demos in demo with python DEMO_NAME.py to see some examples of what this tool does and you also have a Jupyter Notebook demonstrating the 3rd part.

some prints

Tests

There are tests that guarantee 100% coverage (see html version of coverage report here) and there is human friendly documentation here.

  • Run tests: python -m unittest discover
  • Run with coverage: coverage run -m unittest discover
  • Generate (HTML) report: coverage report | coverage html

Docs

To generate the docs again, cd ./docs and:

  • Windows: make.bat html
  • Linux: make html