## PS4 problem 1: suffix bwt algorithm / Burrows Wheeler Transform (BWT)
## The aim of BWT is to map millions of short reads to the genome in O(m) time
## where m is the length of the short read
from SuffixTree import SuffixTree
if __name__ == "__main__":
genome = "MANOLISKELLIS"
bwt = SuffixTree(genome)
sp, ep, bwtsp, bwtep = bwt.findMatch("OLAS")
if sp > 0 and ep > 0:
print("Table ptr locations:")
print("sp = ", sp, ", ep = ", ep)
print("-----")
locations = bwt.getGenomeLocations(bwtsp, bwtep)
print("Genome locations:")
print("bwtsp = ", bwtsp, ", bwtep = ", bwtep)
print(genome)
i, j = 0, 0
while j < len(genome) and i < len(locations):
if locations[i] == j:
print("^", end='')
i += 1
else:
print(" ", end='')
j += 1
