예제 #1
0
def SuffixArray(text, k):
    # generate suffix array
    bwt_genome = sort_matrix(generate_matrix(text))
    suffix_array = bwt_genome[SUFFIX_ARRAY]

    # extract partial suffix array
    partial_suffix_array = list()
    for i in xrange(0, len(suffix_array)):
        if suffix_array[i] % k == 0:
            partial_suffix_array.append([i, suffix_array[i]])
    return partial_suffix_array
예제 #2
0
                results.append(suffix_array[i])
            return results


input = """AATCGGGTTCAATCGGGGT
ATCG
GGGT"""

correct_answer = "1 4 11 15"

split_input = input.split("\n")

string = split_input[0]
patterns = split_input[1:]

bwt_genome = sort_matrix(generate_matrix(string))

suffix_array = bwt_genome[SUFFIX_ARRAY]

last_column = extract_last_column(bwt_genome[MATRIX])

first_column = generate_first_column(last_column)

first_occurrence = generate_first_occurrence(first_column[FIRST_COLUMN])

count = generate_count(last_column, first_column[COLUMN_TYPE])

results = list()
results.extend(
    MultipleBetterBWMatching(
        first_occurrence[FIRST_OCCURRENCE], last_column, patterns[0], count, first_column[COLUMN_TYPE], suffix_array