HW_1 levenshtein distance evaluating tool

A small python script to compute levenshtein distance between nucleotide sequences.

Getting Started

This tool allows you to align sequences and gives you the information about levenshtein distance.

Prerequisites

You need to install python3 with numpy library to run this tool.

Installing

To install this tool clone this repository to your PC.

~$ git clone https://github.com/anton-shikov/HW_1.git

Running and using tool

Using this tool is sa simple as its code is. After downloading repository launch terminal and enter this repository. Use this following to execute tool:

~$ python My_parser_try.py

Note! the following command will run programme with default sequences with corresponding output:

~$ ('ATG', 'CTA', 2.0)

For computing lvenshtein distance for your favourite sequences add flags -sq1 -sq2 . Example:

~$ python My_parser_try.py -sq1 ATTT -sq2 ATGGG
~$ ('ATGGG', 'ATTT_', 3.0)

Output format: corresponding aligned sequences, separeted by coma, symbol _ reflects gaps if they are presented; the number represents levenshtein distance between sequences with equal penalties for insertions, deletions and mismatches.

Author

• Anton Shikov - Initial work - anton-shikov

License

This project is free and available for everyone.

Acknowledgments

Eugene Bakin for python course.