Sequence alignment of Python objects.
Paired is a Python package for pairwise alignment of arbitrary sequences.
Python has lots of great packages for sequence alignment and warping, but mostly for biological or numerical data. Paired performs global alignment on lists of arbitrary Python objects, and lets you define how element pairs are matched and scored.
import paired seq_1 = 'The quick brown fox jumped over the lazy dog'.split(' ') seq_2 = 'The brown fox leaped over the lazy dog'.split(' ') alignment = paired.align(seq_1, seq_2) print(alignment) # [(0, 0), (1, None), (2, 1), (3, 2), (4, 3), (5, 4), (6, 5), (7, 6), (8, 7)] for i_1, i_2 in alignment: print((seq_1[i_1] if i_1 is not None else '').ljust(15), end='') print(seq_2[i_2] if i_2 is not None else '') # The The # quick # brown brown # fox fox # jumped leaped # over over # the the # lazy lazy # dog dog
Paired uses the Needleman-Wunsch algorithm. The scoring for the different operations (match, mismatch, gap) can be specified:
alignment = paired.align(seq_1, seq_2, match_score=5, mismatch_score=-1, gap_score=-5)
By default, two elements are said to match if
element_1 == element_2. Paired also allows you to pass a function to return a match/mismatch score for a given pair of elements. For example, you could give different scores to case-sensitive and case-insensitive matches of strings:
def scorer(a, b): if a == b: return 2 elif a.lower() == b.lower(): return 1 else: return -1 alignment = paired.align(seq_1, seq_2, scorer=scorer, gap_score=-3)
Paired is on PyPi and can be installed with pip. It has no dependencies.
pip install paired
pairwise.align(x, y, match_score=1, mismatch_score=-1, gap_score=-1, scorer=None)
Get the global alignment of two sequences.
- x, y (list): Sequences of objects to align.
- match_score (numeric): Score when matching elements are paired.
- mismatch_score (numeric): Score when mismatching elements are paired.
- gap_score (numeric): Score for an insertion/deletion, when an element is paired with no other element.
- scorer (callable): Function that takes two elements as inputs, and returns a numerical score based on how well they match. If
Noneis passed, the default function used is equivalent to
lamdba a, b: match_score if a==b else mismatch_score.
- alignment (list of tuples): The aligned sequence, as a list of pairs of indices into
yrespectively. A gap is represented by
Noneinstead of an integer index.
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