Python SuffixArray Examples

Example #1

File: tests.py Project: pombredanne/mamaslemonpy

def setup():
    global sa
    indexname = "./gludna"
    sa = SuffixArray.from_indexname(indexname)
    sa.bwt_from_indexname(indexname)
    sa.occ_from_indexname(indexname)
    sa.pos_from_indexname(indexname)
    sa.seq_from_indexname(indexname)

Example #2

File: test_bms.py Project: pombredanne/mamaslemonpy

def main(indexname, num=1000, length=200):
    sa = SuffixArray.from_indexname(indexname)
    sa.bwt_from_indexname(indexname)
    sa.occ_from_indexname(indexname)
    for i in range(num):
        print("PATTERN",i)
        pat, opt = random_pattern(length)
        run_ms(sa, pat, opt)
    pass