205 lines
7.1 KiB
Python
205 lines
7.1 KiB
Python
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import sys
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from collections import namedtuple
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from functools import wraps
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from six.moves import range, zip
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__all__ = [
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'Match', 'Ngram', 'LevenshteinSearchParams',
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'search_exact', 'count_differences_with_maximum',
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'group_matches', 'get_best_match_in_group',
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]
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CLASSES_WITH_INDEX = (list, tuple)
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if sys.version_info >= (3,):
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CLASSES_WITH_FIND = (bytes, str)
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else:
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CLASSES_WITH_FIND = (str, unicode)
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try:
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from Bio.Seq import Seq
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except ImportError:
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pass
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else:
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CLASSES_WITH_FIND += (Seq,)
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Match = namedtuple('Match', ['start', 'end', 'dist'])
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Ngram = namedtuple('Ngram', ['start', 'end'])
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class LevenshteinSearchParams(object):
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def __init__(self,
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max_substitutions=None,
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max_insertions=None,
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max_deletions=None,
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max_l_dist=None):
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self.check_params_valid(max_substitutions, max_insertions,
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max_deletions, max_l_dist)
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self.max_substitutions = max_substitutions
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self.max_insertions = max_insertions
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self.max_deletions = max_deletions
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self.max_l_dist = self._get_max_l_dist(
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max_substitutions, max_insertions,
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max_deletions, max_l_dist,
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)
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@property
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def unpacked(self):
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return self.max_substitutions, self.max_insertions, self.max_deletions, self.max_l_dist
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@classmethod
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def check_params_valid(cls,
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max_substitutions, max_insertions,
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max_deletions, max_l_dist):
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if not all(x is None or (isinstance(x, int) and x >= 0)
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for x in
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[max_substitutions, max_insertions, max_deletions, max_l_dist]):
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raise TypeError("All limits must be positive integers or None.")
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if max_l_dist is None:
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n_limits = (
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(1 if max_substitutions is not None else 0) +
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(1 if max_insertions is not None else 0) +
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(1 if max_deletions is not None else 0)
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)
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if n_limits < 3:
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if n_limits == 0:
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raise ValueError('No limitations given!')
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elif max_substitutions is None:
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raise ValueError('# substitutions must be limited!')
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elif max_insertions is None:
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raise ValueError('# insertions must be limited!')
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elif max_deletions is None:
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raise ValueError('# deletions must be limited!')
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@classmethod
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def _get_max_l_dist(cls,
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max_substitutions, max_insertions,
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max_deletions, max_l_dist):
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bignum = 1 << 29
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maxes_sum = (
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(max_substitutions if max_substitutions is not None else bignum) +
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(max_insertions if max_insertions is not None else bignum) +
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(max_deletions if max_deletions is not None else bignum)
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)
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return (
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max_l_dist
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if max_l_dist is not None and max_l_dist <= maxes_sum
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else maxes_sum
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)
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def search_exact(subsequence, sequence, start_index=0, end_index=None):
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if not subsequence:
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raise ValueError('subsequence must not be empty')
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if end_index is None:
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end_index = len(sequence)
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if isinstance(sequence, CLASSES_WITH_FIND):
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def find_in_index_range(start_index):
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return sequence.find(subsequence, start_index, end_index)
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elif isinstance(sequence, CLASSES_WITH_INDEX):
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first_item = subsequence[0]
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first_item_last_index = end_index - (len(subsequence) - 1)
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def find_in_index_range(start_index):
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while True:
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try:
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first_index = sequence.index(first_item, start_index, first_item_last_index)
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start_index = first_index + 1
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except ValueError:
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return -1
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for subseq_index in range(1, len(subsequence)):
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if sequence[first_index + subseq_index] != subsequence[subseq_index]:
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break
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else:
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return first_index
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else:
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raise TypeError('unsupported sequence type: %s' % type(sequence))
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index = find_in_index_range(start_index)
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while index >= 0:
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yield index
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index = find_in_index_range(index + 1)
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def count_differences_with_maximum(sequence1, sequence2, max_differences):
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n_different = 0
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for item1, item2 in zip(sequence1, sequence2):
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if item1 != item2:
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n_different += 1
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if n_different == max_differences:
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return n_different
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return n_different
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try:
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from fuzzysearch._common import count_differences_with_maximum_byteslike, \
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search_exact_byteslike
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except ImportError:
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pass
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else:
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_count_differences_with_maximum = count_differences_with_maximum
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@wraps(_count_differences_with_maximum)
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def count_differences_with_maximum(sequence1, sequence2, max_differences):
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try:
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return count_differences_with_maximum_byteslike(sequence1,
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sequence2,
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max_differences)
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except TypeError:
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return _count_differences_with_maximum(sequence1, sequence2,
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max_differences)
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_search_exact = search_exact
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@wraps(_search_exact)
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def search_exact(subsequence, sequence, start_index=0, end_index=None):
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if end_index is None:
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end_index = len(sequence)
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try:
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return search_exact_byteslike(subsequence, sequence,
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start_index, end_index)
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except (TypeError, UnicodeEncodeError):
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return _search_exact(subsequence, sequence, start_index, end_index)
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class GroupOfMatches(object):
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def __init__(self, match):
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assert match.start <= match.end
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self.start = match.start
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self.end = match.end
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self.matches = set([match])
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def is_match_in_group(self, match):
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return not (match.end <= self.start or match.start >= self.end)
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def add_match(self, match):
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self.matches.add(match)
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self.start = min(self.start, match.start)
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self.end = max(self.end, match.end)
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def group_matches(matches):
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groups = []
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for match in matches:
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overlapping_groups = [g for g in groups if g.is_match_in_group(match)]
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if not overlapping_groups:
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groups.append(GroupOfMatches(match))
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elif len(overlapping_groups) == 1:
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overlapping_groups[0].add_match(match)
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else:
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new_group = GroupOfMatches(match)
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for group in overlapping_groups:
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for match in group.matches:
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new_group.add_match(match)
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groups = [g for g in groups if g not in overlapping_groups]
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groups.append(new_group)
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return [group.matches for group in groups]
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def get_best_match_in_group(group):
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# return longest match amongst those with the shortest distance
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return min(group, key=lambda match: (match.dist, -(match.end - match.start)))
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