Metadata-Version: 1.1
Name: fuzzysearch
Version: 0.5.0
Summary: fuzzysearch is useful for finding approximate subsequence matches
Home-page: https://github.com/taleinat/fuzzysearch
Author: Tal Einat
Author-email: taleinat@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: ===============================
        fuzzysearch
        ===============================
        
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            :target: https://pypi.python.org/pypi/fuzzysearch
            :alt: Latest Version
        
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            :alt: Test Coverage
        
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            :alt: Downloads
        
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            :alt: Wheels
        
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            :alt: Supported Python versions
        
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            :alt: Supported Python implementations
        
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            :target: https://pypi.python.org/pypi/fuzzysearch/
            :alt: License
        
        fuzzysearch is a Python library for fuzzy substring searches. It implements efficient
        ad-hoc searching for approximate sub-sequences. Matching is done using a generalized
        Levenshtein Distance metric, with configurable parameters.
        
        * Free software: `MIT license <LICENSE>`_
        * Documentation: http://fuzzysearch.rtfd.org.
        
        Installation
        ------------
        Just install using pip::
        
            $ pip install fuzzysearch
        
        Features
        --------
        
        * Fuzzy sub-sequence search: Find parts of a sequence which match a given
          sub-sequence.
        * Easy to use: A single function to call which returns a list of matches.
        * Set a maximum Levenshtein Distance for matches, including individual limits
          for the number of substitutions, insertions and/or deletions allowed for
          near-matches.
        * Includes optimized implementations for specific use-cases, e.g. allowing
          only substitutions.
        
        Simple Examples
        ---------------
        Just call `find_near_matches()` with the sequence to search, the sub-sequence
        you're looking for, 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)]
        
        .. 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)]
        
        Advanced Search Criteria
        ------------------------
        The search function supports four possible match criteria, which may be supplied in any combination:
        
        * maximum Levenshtein distance
        * maximum # of subsitutions
        * maximum # of deletions (elements appearing in the pattern search for, which are skipped in the matching sub-sequence)
        * maximum # of insertions (elements added in the matching sub-sequence which don't appear in the pattern search for)
        
        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)]
            
            # 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)] # 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)]
        
        
        
        
        History
        -------
        
        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.
Keywords: fuzzysearch
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Software Development :: Libraries :: Python Modules
