Python implementation of Suffix Trees and Generalized Suffix Trees for sequence (list) of integers and for the evaluation of the covering similarity. This code has been derived from Peter Us (petrus) implementation of generalized suffix trees available at https://github.com/ptrus/suffix-trees, under The MIT License (MIT).
In the install directory:
$ python3 setup.py install
or
$ pip3 install git+https://github.com/pfmarteau/STree4CS
from STree4CS import STree4CS as STree
# Suffix-Tree example.
st = STree.STree4CS([[1, 10, 5, 3, 200, 8, 10, 2]])
print(st.find([1, 10])) # 0
print(st.find_all([10])) # [1, 6]
# Building a generalized Suffix-Tree.
A = [[1, 2, 3], [4, 5, 6, 2, 3, 7], [1, 2, 3, 4]]
st = STree.STree4CS(A)
# print the longest common subsequence for the set A
print(st.lcs()) # [2, 3]
# Sequence Covering similarity example
S=[[1,1,2,2,3,4,1,1,5,6], [1,2,4,3,4,5,7,5,1], [6,5,1,7,4,5,6]]
s=[1,1,5,7,5,1,7,4]
# Build the generalized Suffix-Tree for S
st = STree.STree4CS(S)
# get the S-optimal covering similarity for s
score, lbreak, lss = st.evaluateDichotomic(s)
print(score) # 0.75
print(lss) # the optimal covering [[1, 1, 5], [7, 5, 1], [7, 4]], This library is mostly an academic exercise. If you need an efficient library I would recommend a python-wrapped c implementation, such as (http://www.daimi.au.dk/~mailund/suffix_tree.html).