bmiao10 / project1

Project 1 - Sequence Alignment

Due 01/27/2021

In this assignment, you will implement two classical alignment algorithms and then evaluate each algorithm’s performance with a range of parameters. There are two parts to this assignment and Part 2 requires completion of Part 1. We recommend reading through both Part 1 and Part 2 before beginning this assignment.

• Part 1 - API and implementation
• Part 2 - Evaluating alignments

file structure

.
├── README.md
├── Brenda_Miao_BMI203_HW1.ipynb
│   ...
├── align
│   ├── __init__.py
│   ├── __main__.py
│   └── algs.py
│  
├── docs
│   └── build
│   	  └── html
│              └── index.html
│   ...
├── output
│   ├── Q2-1_pair_scores.csv
│   ├── Q2-5_values.csv
│   └── Q2-6_scores.csv
└── test
    └── test_align.py

sphinx documentation

Located in docs folder

part I and II

Code, figures, and questions are answered in Jupyter notebook Output for certain questions are stored in output folder

testing

Testing is as simple as running

python -m pytest

from the root directory of this project.