benhid / NeedlemanWunschPy

This code is meant for educational purposes only! Sequence alignment in Python 3.x using Needleman–Wunsch algorithm. Reference code from TyMA (2017 - University of Málaga)

NeedlemanWunschPy

Implementation of the Needleman-Wunsch algorithm in Python 3.x

Dependencies

We use NumPy and pandas for matrix manipulations.

$ pip install pandas
$ pip install numpy

However, we recommend downloading the latest version of Anaconda as it includes several packages (like NumPy and pandas) by default.

Usage

An example is shown in example.py.

Output

The output will be created on a directory called output/. This will include:

1. The score matrix (score_matrix.csv) only if save_score_matrix_to_file was set to True.
2. A log file (output.log) including the time of execution of the program (you can also set level to DEBUG inside logconfig.ini/[handler_default] to show the traceback path).