CS325 Homework 2 Implementation

Private git repo for our second homework implementation project in analysis of algorithms

HOW TO USE

Options:

The program has optional parameters when run:

• -c <cost_file> will use the provided file as the cost matrix for calculations. Defaults to "imp2cost.txt" if not specified
• -i <input_file> will use the provided file as the input for the sequences. Defaults to "imp2input.txt" if not specified
• -o <output_file> will use the provided file as the output. Defaults to "imp2output.txt" if not specified

Run with Provided Input:

To run the program with the provided input file, run the command python seq_align.py. This will use the default file names "imp2input.txt" and "imp2cost.txt" and create a file named "imp2output.txt".

To ensure that this output is correct, run the command python check_cost.py. This will use the default file names "imp2output.txt" and "imp2cost.txt" and create a file named "cost_check_results.txt", detailing all the checks and whether or not they were passed.

Run with Random Input:

To run the program with a random input file, run the command python input_gen.py <size of desired input>. This will create a file named "imp2input-<size of desired input>.txt".

To run the "seq_align.py" file with this new input file, run the command python seq_align.py -i imp2input-<size of desired input>.txt. Continue from the Provided Input section above.

For example, if one wanted to use a file size of 1000, the steps they would take are:

1. Run python input_gen.py 1000
2. Run python seq_align.py -i imp2input-1000.txt
3. Run python check_cost.py