from DNAHelper.helper_functions import *
from SuffixTree import SuffixTree
alphabet = 'AGTCN'
text = read_genome('../Dataset/phix.fa')
reads, qualities = read_fastq('../Dataset/phix.fastq')
tree = SuffixTree(alphabet)
tree.build_generalized_suffix_tree([text])
count = 0
matches = []
for read in reads:
read = read[:30]
matches = tree.find(read)
matches.extend(tree.find(reverse_complement(read)))
if len(matches) > 0:
count += 1
print(count, '/', len(reads), 'matched!')
