pylcs 0.1.1

super fast cpp implementation of longest common subsequence

pylcs

The original repository stop maintenance. This is a transfer version

pylcs is a super fast c++ library which adopts dynamic programming(DP) algorithm to solve two classic LCS problems as below .

The longest common subsequence problem is the problem of finding the longest subsequence common to all sequences in a set of sequences (often just two sequences).

The longest common substring problem is to find the longest string (or strings) that is a substring (or are substrings) of two or more strings.

Levenshtein distance, aka edit distance is also supported. Emm...forget the package name. Example usage is in tests.

We also support Chinese(or any UTF-8) string.

Colorful Visualization: After 0.1.0, you can visualize the lcs result with colorful output.

Install

To install, simply do pip install pylcs to pull down the latest version from PyPI.

Python code example

import pylcs

#  finding the longest common subsequence length of string A and string B
A = 'We are shannonai'
B = 'We like shannonai'
pylcs.lcs_sequence_length(A, B)
"""
>>> pylcs.lcs_sequence_length(A, B)
14
"""

#  finding alignment from string A to B
A = 'We are shannonai'
B = 'We like shannonai'
res = pylcs.lcs_sequence_idx(A, B)
''.join([B[i] for i in res if i != -1])
"""
>>> res
[0, 1, 2, -1, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]
>>> ''.join([B[i] for i in res if i != -1])
'We e shannonai'
"""

#  finding the longest common subsequence length of string A and a list of string B
A = 'We are shannonai'
B = ['We like shannonai', 'We work in shannonai', 'We are not shannonai']
pylcs.lcs_sequence_of_list(A, B)
"""
>>> pylcs.lcs_sequence_of_list(A, B)
[14, 14, 16]
"""

# finding the longest common substring length of string A and string B
A = 'We are shannonai'
B = 'We like shannonai'
pylcs.lcs_string_length(A, B)
"""
>>> pylcs.lcs_string_length(A, B)
11
"""

#  finding alignment from string A to B
A = 'We are shannonai'
B = 'We like shannonai'
res = pylcs.lcs_string_idx(A, B)
''.join([B[i] for i in res if i != -1])
"""
>>> res
[-1, -1, -1, -1, -1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]
>>> ''.join([B[i] for i in res if i != -1])
'e shannonai'
"""

#  finding the longest common substring length of string A and a list of string B
A = 'We are shannonai'
B = ['We like shannonai', 'We work in shannonai', 'We are not shannonai']
pylcs.lcs_string_of_list(A, B)
"""
>>> pylcs.lcs_string_of_list(A, B)
[11, 10, 10]
"""

#  finding the weighted edit distance from string A to B
pylcs.edit_distance("aaa", "aba")
pylcs.edit_distance("aaa", "aba", {'a': {'b': 2.0}})
pylcs.edit_distance("", "aa", {'': {'a': 0.5}})
#  weight['']['a'] means inserting a char 'a' costs 0.5
#  similarly, weight['a'][''] means the score of deleting a char 'a'
"""
>>> pylcs.edit_distance("aaa", "aba")
1
>>> pylcs.edit_distance("aaa", "aba", {'a': {'b': 2.0}})
2.0
>>> pylcs.edit_distance("", "aa", {'': {'a': 0.5}})
1.0
"""

#  finding edit distance alignment from string A to B
pylcs.edit_distance_idx("aaa", "aba")
pylcs.edit_distance_idx("aaa", "aba", {'a': {'b': 3}})
pylcs.edit_distance_idx("aa", "aabb", {'a': {'a': 2, 'b': 0}})
"""
>>> pylcs.edit_distance_idx("aaa", "aba")
[0, 1, 2]
>>> pylcs.edit_distance_idx("aaa", "aba", {'a': {'b': 3}})
[0, -1, 2]
>>> pylcs.edit_distance_idx("aa", "aabb", {'a': {'a': 2, 'b': 0}})
[2, 3]
"""

After 0.1.0, you can make a visualized comparison with colorful output. Using coloring_match_sequence to color the s1 and s2 by a match list like:

s1, s2 = "abcdefghijklmnopq", "-c-fgh-kl-nop-q"
match_list = pylcs.lcs_sequence_idx(s1, s2)
colored_s1, colored_s2 = pylcs.coloring_match_sequence(match_list, s1, s2, 11, 11, "#2266ff", "#2266ff", t=1)
print(colored_s1, colored_s2)
colored_s1, colored_s2 = pylcs.coloring_match_sequence(match_list, s1, s2, 11, 11, "#2266ff", "#2266ff", t=2)
print(colored_s1, colored_s2)
colored_s1, colored_s2 = pylcs.coloring_match_sequence(match_list, s1, s2, 11, 11, "#2266ff", "#2266ff", t=3)
print(colored_s1, colored_s2)

s1, s2 = "How does this string edit to s2?", "How similar is this string to s1?"
match_list = pylcs.edit_distance_idx(s1, s2)
colored_s1, colored_s2 = pylcs.coloring_match_sequence(match_list, s1, s2, 4, 4, 230, 230, t=2)
print(colored_s1, colored_s2, sep='\n')

Note that the colorful output uses ANSI escape codes. Referring to https://en.wikipedia.org/wiki/ANSI_escape_code.

The ANSI codes may not work in win32 command line.