===========
fuzzysearch
===========
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Fuzzy search: Find parts of long text or data, allowing for some
changes/typos.
**Easy, fast, and just works!**
.. code:: python
>>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)
[Match(start=3, end=9, dist=1, matched="PATERN")]
* Two simple functions to use: one for in-memory data and one for files
* Fastest search algorithm is chosen automatically
* Levenshtein Distance metric with configurable parameters
* Separately configure the max. allowed distance, substitutions, deletions
and/or insertions
* Advanced algorithms with optional C and Cython optimizations
* Properly handles Unicode; special optimizations for binary data
* Simple installation:
* ``pip install fuzzysearch`` just works
* pure-Python fallbacks for compiled modules
* only one dependency (``attrs``)
* Extensively tested
* Free software: `MIT license <LICENSE>`_
For more info, see the `documentation <http://fuzzysearch.rtfd.org>`_.
Installation
------------
``fuzzysearch`` supports Python versions 3.8+, as well as PyPy 3.9 and 3.10.
.. code::
$ pip install fuzzysearch
This will work even if installing the C and Cython extensions fails, using
pure-Python fallbacks.
Usage
-----
Just call ``find_near_matches()`` with the sub-sequence you're looking for,
the sequence to search, and the matching parameters:
.. code:: python
>>> from fuzzysearch import find_near_matches
# search for 'PATTERN' with a maximum Levenshtein Distance of 1
>>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)
[Match(start=3, end=9, dist=1, matched="PATERN")]
To search in a file, use ``find_near_matches_in_file()`` similarly:
.. code:: python
>>> from fuzzysearch import find_near_matches_in_file
>>> with open('data_file', 'rb') as f:
... find_near_matches_in_file(b'PATTERN', f, max_l_dist=1)
[Match(start=3, end=9, dist=1, matched="PATERN")]
Examples
--------
*fuzzysearch* is great for ad-hoc searches of genetic data, such as DNA or
protein sequences, before reaching for "heavier", domain-specific tools like
BioPython:
.. code:: python
>>> sequence = '''\
GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGTCACACACACA
TTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACACATTAGACGCGTACATAGACA
CAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATACTCGCGTAGTCGTGGGAGGCAAGGCACACAG
GGGATAGG'''
>>> subsequence = 'TGCACTGTAGGGATAACAAT' # distance = 1
>>> find_near_matches(subsequence, sequence, max_l_dist=2)
[Match(start=3, end=24, dist=1, matched="TAGCACTGTAGGGATAACAAT")]
BioPython sequences are also supported:
.. code:: python
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> sequence = Seq('''\
GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGTCACACACACA
TTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACACATTAGACGCGTACATAGACA
CAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATACTCGCGTAGTCGTGGGAGGCAAGGCACACAG
GGGATAGG''', IUPAC.unambiguous_dna)
>>> subsequence = Seq('TGCACTGTAGGGATAACAAT', IUPAC.unambiguous_dna)
>>> find_near_matches(subsequence, sequence, max_l_dist=2)
[Match(start=3, end=24, dist=1, matched="TAGCACTGTAGGGATAACAAT")]
Matching Criteria
-----------------
The search function supports four possible match criteria, which may be
supplied in any combination:
* maximum Levenshtein distance (``max_l_dist``)
* maximum # of subsitutions
* maximum # of deletions ("delete" = skip a character in the sub-sequence)
* maximum # of insertions ("insert" = skip a character in the sequence)
Not supplying a criterion means that there is no limit for it. For this reason,
one must always supply ``max_l_dist`` and/or all other criteria.
.. code:: python
>>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)
[Match(start=3, end=9, dist=1, matched="PATERN")]
# this will not match since max-deletions is set to zero
>>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1, max_deletions=0)
[]
# note that a deletion + insertion may be combined to match a substution
>>> find_near_matches('PATTERN', '---PAT-ERN---', max_deletions=1, max_insertions=1, max_substitutions=0)
[Match(start=3, end=10, dist=1, matched="PAT-ERN")] # the Levenshtein distance is still 1
# ... but deletion + insertion may also match other, non-substitution differences
>>> find_near_matches('PATTERN', '---PATERRN---', max_deletions=1, max_insertions=1, max_substitutions=0)
[Match(start=3, end=10, dist=2, matched="PATERRN")]
When to Use Other Tools
-----------------------
* Use case: Search through a list of strings for almost-exactly matching
strings. For example, searching through a list of names for possible slight
variations of a certain name.
Suggestion: Consider using `fuzzywuzzy <https://github.com/seatgeek/fuzzywuzzy>`_.
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