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# -*- coding: utf-8 -*- |
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# Copyright 2014-2018 by Christopher C. Little. |
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# This file is part of Abydos. |
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# |
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# Abydos is free software: you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation, either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# Abydos is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with Abydos. If not, see <http://www.gnu.org/licenses/>. |
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"""abydos.distance._ncd_bwtrle. |
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NCD using BWT plus RLE |
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""" |
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from __future__ import ( |
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absolute_import, |
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division, |
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print_function, |
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unicode_literals, |
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) |
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from ._ncd_rle import NCDrle |
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from ..compression import BWT |
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__all__ = ['NCDbwtrle', 'dist_ncd_bwtrle', 'sim_ncd_bwtrle'] |
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class NCDbwtrle(NCDrle): |
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"""Normalized Compression Distance using BWT plus RLE. |
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Cf. https://en.wikipedia.org/wiki/Burrows-Wheeler_transform |
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Normalized compression distance (NCD) :cite:`Cilibrasi:2005`. |
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""" |
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_bwt = BWT() |
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def dist(self, src, tar): |
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"""Return the NCD between two strings using BWT plus RLE. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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Compression distance |
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Examples |
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-------- |
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>>> cmp = NCDbwtrle() |
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>>> cmp.dist('cat', 'hat') |
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0.75 |
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>>> cmp.dist('Niall', 'Neil') |
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0.8333333333333334 |
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>>> cmp.dist('aluminum', 'Catalan') |
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1.0 |
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>>> cmp.dist('ATCG', 'TAGC') |
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0.8 |
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""" |
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if src == tar: |
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return 0.0 |
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src_comp = self._rle.encode(self._bwt.encode(src)) |
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tar_comp = self._rle.encode(self._bwt.encode(tar)) |
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concat_comp = self._rle.encode(self._bwt.encode(src + tar)) |
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concat_comp2 = self._rle.encode(self._bwt.encode(tar + src)) |
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return ( |
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min(len(concat_comp), len(concat_comp2)) |
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- min(len(src_comp), len(tar_comp)) |
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) / max(len(src_comp), len(tar_comp)) |
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def dist_ncd_bwtrle(src, tar): |
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"""Return the NCD between two strings using BWT plus RLE. |
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This is a wrapper for :py:meth:`NCDbwtrle.dist`. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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Compression distance |
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Examples |
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-------- |
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>>> dist_ncd_bwtrle('cat', 'hat') |
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0.75 |
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>>> dist_ncd_bwtrle('Niall', 'Neil') |
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0.8333333333333334 |
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>>> dist_ncd_bwtrle('aluminum', 'Catalan') |
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1.0 |
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>>> dist_ncd_bwtrle('ATCG', 'TAGC') |
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0.8 |
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""" |
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return NCDbwtrle().dist(src, tar) |
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def sim_ncd_bwtrle(src, tar): |
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"""Return the NCD similarity between two strings using BWT plus RLE. |
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This is a wrapper for :py:meth:`NCDbwtrle.sim`. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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Returns |
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------- |
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float |
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Compression similarity |
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Examples |
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-------- |
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>>> sim_ncd_bwtrle('cat', 'hat') |
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0.25 |
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>>> sim_ncd_bwtrle('Niall', 'Neil') |
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0.16666666666666663 |
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>>> sim_ncd_bwtrle('aluminum', 'Catalan') |
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0.0 |
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>>> sim_ncd_bwtrle('ATCG', 'TAGC') |
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0.19999999999999996 |
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""" |
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return NCDbwtrle().sim(src, tar) |
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if __name__ == '__main__': |
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import doctest |
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doctest.testmod() |
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chrislit /
abydos
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