Description of files

• pj4.py - the implementation of PatternMatchingWithSuffixArray and BetterBWMatching; instruction to run can be found bellow

Instruction to Run pj4.py

The script "pj4.py" can be run from shell.

First edit the first line of this script (#!/usr/local/cs/bin/python3) to make sure that it is invoking Python from the correct directory in your environment.

Then give execution permission using commands like:
chmod 744 ./pj4.py

Then the script can be run with the following syntax.
./pj4.py [NUM_READS] [LEN_READ] [LEN_GENOME] [WHICH_ALGORITHM] where:

NUM_READS - number of reads
LEN_READ - length of each read
LEN_GENOME - length of the genome
WHICH_ALGORITHM - which algorithm to perform:
	'0' for PatternMatchingWithSuffixArray
	'1' for BetterBWMatching
	'2' for checking if the two algorithms's results agree

For example, ./pj4.py 100000 100 500000 0 means apply PatternMatchingWithSuffixArray to a genome of length 500,000 with 100,000 reads all of which are of length 100.

Some expected output:

$ ./pj4.py 100 10 100 0
PatternMatchingWithSuffixArray:
- runtime: 0.001786947250366211 seconds
- results: 100 matches found
- current memory usage: 0.010112MB; peak: 0.030255MB
$ ./pj4.py 100 10 100 1
BetterBWMatching:
- runtime: 0.0014259815216064453 seconds
- results: 100 matches found
- current memory usage: 0.0142MB; peak: 0.035407MB
$ ./pj4.py 100 10 100 2
Success. Results from the two algorithms matches