===========
fuzzysearch
===========
.. image:: https://img.shields.io/pypi/v/fuzzysearch.svg?style=flat
:target: https://pypi.python.org/pypi/fuzzysearch
:alt: Latest Version
.. image:: https://img.shields.io/travis/taleinat/fuzzysearch.svg?branch=master
:target: https://travis-ci.org/taleinat/fuzzysearch/branches
:alt: Build & Tests Status
.. image:: https://img.shields.io/coveralls/taleinat/fuzzysearch.svg?branch=master
:target: https://coveralls.io/r/taleinat/fuzzysearch?branch=master
:alt: Test Coverage
.. image:: https://img.shields.io/pypi/wheel/fuzzysearch.svg?style=flat
:target: https://pypi.python.org/pypi/fuzzysearch
:alt: Wheels
.. image:: https://img.shields.io/pypi/pyversions/fuzzysearch.svg?style=flat
:target: https://pypi.python.org/pypi/fuzzysearch
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/implementation/fuzzysearch.svg?style=flat
:target: https://pypi.python.org/pypi/fuzzysearch
:alt: Supported Python implementations
.. image:: https://img.shields.io/pypi/l/fuzzysearch.svg?style=flat
:target: https://pypi.python.org/pypi/fuzzysearch/
:alt: License
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 2.7 and 3.5+, as well as PyPy 2.7 and
3.6.
.. 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>`_.
History
-------
0.7.3 (2020-06-27)
++++++++++++++++++
* Fixed segmentation faults due to wrong handling of inputs in bytes-like-only
functions in C extensions.
0.7.2 (2020-05-07)
++++++++++++++++++
* Added PyPy support.
* Several minor bug fixes.
0.7.1 (2020-04-05)
++++++++++++++++++
* Dropped support for Python 3.4.
* Removed deprecation warning with Python 3.8.
* Fixed a couple of nasty bugs.
0.7.0 (2020-01-14)
++++++++++++++++++
* Added ``matched`` attribue to ``Match`` objects containing the matched part
of the sequence.
* Added support for CPython 3.8. Now supporting CPython 2.7 and 3.4-3.8.
0.6.2 (2019-04-22)
++++++++++++++++++
* Fix calling ``search_exact()`` without passing ``end_index``.
* Fix edge case: max. dist >= sub-sequence length.
0.6.1 (2018-12-08)
++++++++++++++++++
* Fixed some C compiler warnings for the C and Cython modules
0.6.0 (2018-12-07)
++++++++++++++++++
* Dropped support for Python versions 2.6, 3.2 and 3.3
* Added support and testing for Python 3.7
* Optimized the n-grams Levenshtein search for long sub-sequences
* Further optimized the n-grams Levenshtein search
* Cython versions of the optimized parts of the n-grams Levenshtein search
0.5.0 (2017-09-05)
++++++++++++++++++
* Fixed ``search_exact_byteslike()`` to support supplying start and end indexes
* Added support for lists, tuples and other Sequence types to ``search_exact()``
* Fixed a bug where ``find_near_matches()`` could return a wrong ``Match.end``
with ``max_l_dist=0``
* Added more tests and improved some existing ones.
0.4.0 (2017-07-06)
++++++++++++++++++
* Added support and testing for Python 3.5 and 3.6
* Many small improvements to README, setup.py and CI testing
0.3.0 (2015-02-12)
++++++++++++++++++
* Added C extensions for several search functions as well as internal functions
* Use C extensions if available, or pure-Python implementations otherwise
* setup.py attempts to build C extensions, but installs without if build fails
* Added ``--noexts`` setup.py option to avoid trying to build the C extensions
* Greatly improved testing and coverage
0.2.2 (2014-03-27)
++++++++++++++++++
* Added support for searching through BioPython Seq objects
* Added specialized search function allowing only subsitutions and insertions
* Fixed several bugs
0.2.1 (2014-03-14)
++++++++++++++++++
* Fixed major match grouping bug
0.2.0 (2013-03-13)
++++++++++++++++++
* New utility function ``find_near_matches()`` for easier use
* Additional documentation
0.1.0 (2013-11-12)
++++++++++++++++++
* Two working implementations
* Extensive test suite; all tests passing
* Full support for Python 2.6-2.7 and 3.1-3.3
* Bumped status from Pre-Alpha to Alpha
0.0.1 (2013-11-01)
++++++++++++++++++
* First release on PyPI.
Raw data
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"description": "===========\nfuzzysearch\n===========\n\n.. image:: https://img.shields.io/pypi/v/fuzzysearch.svg?style=flat\n :target: https://pypi.python.org/pypi/fuzzysearch\n :alt: Latest Version\n\n.. image:: https://img.shields.io/travis/taleinat/fuzzysearch.svg?branch=master\n :target: https://travis-ci.org/taleinat/fuzzysearch/branches\n :alt: Build & Tests Status\n\n.. image:: https://img.shields.io/coveralls/taleinat/fuzzysearch.svg?branch=master\n :target: https://coveralls.io/r/taleinat/fuzzysearch?branch=master\n :alt: Test Coverage\n\n.. image:: https://img.shields.io/pypi/wheel/fuzzysearch.svg?style=flat\n :target: https://pypi.python.org/pypi/fuzzysearch\n :alt: Wheels\n\n.. image:: https://img.shields.io/pypi/pyversions/fuzzysearch.svg?style=flat\n :target: https://pypi.python.org/pypi/fuzzysearch\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/implementation/fuzzysearch.svg?style=flat\n :target: https://pypi.python.org/pypi/fuzzysearch\n :alt: Supported Python implementations\n\n.. image:: https://img.shields.io/pypi/l/fuzzysearch.svg?style=flat\n :target: https://pypi.python.org/pypi/fuzzysearch/\n :alt: License\n\nFuzzy search: Find parts of long text or data, allowing for some\nchanges/typos.\n\n**Easy, fast, and just works!**\n\n.. code:: python\n\n >>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)\n [Match(start=3, end=9, dist=1, matched=\"PATERN\")]\n\n* Two simple functions to use: one for in-memory data and one for files\n\n * Fastest search algorithm is chosen automatically\n\n* Levenshtein Distance metric with configurable parameters\n\n * Separately configure the max. allowed distance, substitutions, deletions\n and/or insertions\n\n* Advanced algorithms with optional C and Cython optimizations\n\n* Properly handles Unicode; special optimizations for binary data\n\n* Simple installation:\n * ``pip install fuzzysearch`` just works\n * pure-Python fallbacks for compiled modules\n * only one dependency (``attrs``)\n\n* Extensively tested\n\n* Free software: `MIT license <LICENSE>`_\n\nFor more info, see the `documentation <http://fuzzysearch.rtfd.org>`_.\n\n\nInstallation\n------------\n\n``fuzzysearch`` supports Python versions 2.7 and 3.5+, as well as PyPy 2.7 and\n3.6.\n\n.. code::\n\n $ pip install fuzzysearch\n\nThis will work even if installing the C and Cython extensions fails, using\npure-Python fallbacks.\n\n\nUsage\n-----\nJust call ``find_near_matches()`` with the sub-sequence you're looking for,\nthe sequence to search, and the matching parameters:\n\n.. code:: python\n\n >>> from fuzzysearch import find_near_matches\n # search for 'PATTERN' with a maximum Levenshtein Distance of 1\n >>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)\n [Match(start=3, end=9, dist=1, matched=\"PATERN\")]\n\nTo search in a file, use ``find_near_matches_in_file()`` similarly:\n\n.. code:: python\n\n >>> from fuzzysearch import find_near_matches_in_file\n >>> with open('data_file', 'rb') as f:\n ... find_near_matches_in_file(b'PATTERN', f, max_l_dist=1)\n [Match(start=3, end=9, dist=1, matched=\"PATERN\")]\n\n\nExamples\n--------\n\n*fuzzysearch* is great for ad-hoc searches of genetic data, such as DNA or\nprotein sequences, before reaching for \"heavier\", domain-specific tools like\nBioPython:\n\n.. code:: python\n\n >>> sequence = '''\\\n GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGTCACACACACA\n TTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACACATTAGACGCGTACATAGACA\n CAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATACTCGCGTAGTCGTGGGAGGCAAGGCACACAG\n GGGATAGG'''\n >>> subsequence = 'TGCACTGTAGGGATAACAAT' # distance = 1\n >>> find_near_matches(subsequence, sequence, max_l_dist=2)\n [Match(start=3, end=24, dist=1, matched=\"TAGCACTGTAGGGATAACAAT\")]\n\nBioPython sequences are also supported:\n\n.. code:: python\n\n >>> from Bio.Seq import Seq\n >>> from Bio.Alphabet import IUPAC\n >>> sequence = Seq('''\\\n GACTAGCACTGTAGGGATAACAATTTCACACAGGTGGACAATTACATTGAAAATCACAGATTGGTCACACACACA\n TTGGACATACATAGAAACACACACACATACATTAGATACGAACATAGAAACACACATTAGACGCGTACATAGACA\n CAAACACATTGACAGGCAGTTCAGATGATGACGCCCGACTGATACTCGCGTAGTCGTGGGAGGCAAGGCACACAG\n GGGATAGG''', IUPAC.unambiguous_dna)\n >>> subsequence = Seq('TGCACTGTAGGGATAACAAT', IUPAC.unambiguous_dna)\n >>> find_near_matches(subsequence, sequence, max_l_dist=2)\n [Match(start=3, end=24, dist=1, matched=\"TAGCACTGTAGGGATAACAAT\")]\n\n\nMatching Criteria\n-----------------\nThe search function supports four possible match criteria, which may be\nsupplied in any combination:\n\n* maximum Levenshtein distance (``max_l_dist``)\n\n* maximum # of subsitutions\n\n* maximum # of deletions (\"delete\" = skip a character in the sub-sequence)\n\n* maximum # of insertions (\"insert\" = skip a character in the sequence)\n\nNot supplying a criterion means that there is no limit for it. For this reason,\none must always supply ``max_l_dist`` and/or all other criteria.\n\n.. code:: python\n\n >>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1)\n [Match(start=3, end=9, dist=1, matched=\"PATERN\")]\n\n # this will not match since max-deletions is set to zero\n >>> find_near_matches('PATTERN', '---PATERN---', max_l_dist=1, max_deletions=0)\n []\n\n # note that a deletion + insertion may be combined to match a substution\n >>> find_near_matches('PATTERN', '---PAT-ERN---', max_deletions=1, max_insertions=1, max_substitutions=0)\n [Match(start=3, end=10, dist=1, matched=\"PAT-ERN\")] # the Levenshtein distance is still 1\n\n # ... but deletion + insertion may also match other, non-substitution differences\n >>> find_near_matches('PATTERN', '---PATERRN---', max_deletions=1, max_insertions=1, max_substitutions=0)\n [Match(start=3, end=10, dist=2, matched=\"PATERRN\")]\n\n\nWhen to Use Other Tools\n-----------------------\n\n* Use case: Search through a list of strings for almost-exactly matching\n strings. For example, searching through a list of names for possible slight\n variations of a certain name.\n\n Suggestion: Consider using `fuzzywuzzy <https://github.com/seatgeek/fuzzywuzzy>`_.\n\n\n\n\nHistory\n-------\n\n0.7.3 (2020-06-27)\n++++++++++++++++++\n\n* Fixed segmentation faults due to wrong handling of inputs in bytes-like-only\n functions in C extensions.\n\n0.7.2 (2020-05-07)\n++++++++++++++++++\n* Added PyPy support.\n* Several minor bug fixes.\n\n0.7.1 (2020-04-05)\n++++++++++++++++++\n* Dropped support for Python 3.4.\n* Removed deprecation warning with Python 3.8.\n* Fixed a couple of nasty bugs.\n\n0.7.0 (2020-01-14)\n++++++++++++++++++\n\n* Added ``matched`` attribue to ``Match`` objects containing the matched part\n of the sequence.\n* Added support for CPython 3.8. Now supporting CPython 2.7 and 3.4-3.8.\n\n0.6.2 (2019-04-22)\n++++++++++++++++++\n\n* Fix calling ``search_exact()`` without passing ``end_index``.\n* Fix edge case: max. dist >= sub-sequence length.\n\n0.6.1 (2018-12-08)\n++++++++++++++++++\n\n* Fixed some C compiler warnings for the C and Cython modules\n\n0.6.0 (2018-12-07)\n++++++++++++++++++\n\n* Dropped support for Python versions 2.6, 3.2 and 3.3\n* Added support and testing for Python 3.7\n* Optimized the n-grams Levenshtein search for long sub-sequences\n* Further optimized the n-grams Levenshtein search\n* Cython versions of the optimized parts of the n-grams Levenshtein search\n\n0.5.0 (2017-09-05)\n++++++++++++++++++\n\n* Fixed ``search_exact_byteslike()`` to support supplying start and end indexes\n* Added support for lists, tuples and other Sequence types to ``search_exact()``\n* Fixed a bug where ``find_near_matches()`` could return a wrong ``Match.end``\n with ``max_l_dist=0``\n* Added more tests and improved some existing ones.\n\n0.4.0 (2017-07-06)\n++++++++++++++++++\n\n* Added support and testing for Python 3.5 and 3.6\n* Many small improvements to README, setup.py and CI testing\n\n0.3.0 (2015-02-12)\n++++++++++++++++++\n\n* Added C extensions for several search functions as well as internal functions\n* Use C extensions if available, or pure-Python implementations otherwise\n* setup.py attempts to build C extensions, but installs without if build fails\n* Added ``--noexts`` setup.py option to avoid trying to build the C extensions\n* Greatly improved testing and coverage\n\n0.2.2 (2014-03-27)\n++++++++++++++++++\n\n* Added support for searching through BioPython Seq objects\n* Added specialized search function allowing only subsitutions and insertions\n* Fixed several bugs\n\n0.2.1 (2014-03-14)\n++++++++++++++++++\n\n* Fixed major match grouping bug\n\n0.2.0 (2013-03-13)\n++++++++++++++++++\n\n* New utility function ``find_near_matches()`` for easier use\n* Additional documentation\n\n0.1.0 (2013-11-12)\n++++++++++++++++++\n\n* Two working implementations\n* Extensive test suite; all tests passing\n* Full support for Python 2.6-2.7 and 3.1-3.3\n* Bumped status from Pre-Alpha to Alpha\n\n0.0.1 (2013-11-01)\n++++++++++++++++++\n\n* First release on PyPI.\n\n",
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