msramalho / fcup-abi

Algorithms for Bionformatics - Python Module to handle biological sequences and run common algorithms and techniques

Fcup ABI

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

• 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.

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