Add local version of the counter class

src/obitools/collections.py

@@ -0,0 +1,190 @@
+from operator import itemgetter
+from heapq import nlargest
+from itertools import repeat, ifilter
+
+class Counter(dict):
+    '''Dict subclass for counting hashable objects.  Sometimes called a bag
+    or multiset.  Elements are stored as dictionary keys and their counts
+    are stored as dictionary values.
+
+    >>> Counter('zyzygy')
+    Counter({'y': 3, 'z': 2, 'g': 1})
+
+    '''
+
+    def __init__(self, iterable=None, **kwds):
+        '''Create a new, empty Counter object.  And if given, count elements
+        from an input iterable.  Or, initialize the count from another mapping
+        of elements to their counts.
+
+        >>> c = Counter()                           # a new, empty counter
+        >>> c = Counter('gallahad')                 # a new counter from an iterable
+        >>> c = Counter({'a': 4, 'b': 2})           # a new counter from a mapping
+        >>> c = Counter(a=4, b=2)                   # a new counter from keyword args
+
+        '''        
+        self.update(iterable, **kwds)
+
+    def __missing__(self, key):
+        return 0
+
+    def most_common(self, n=None):
+        '''List the n most common elements and their counts from the most
+        common to the least.  If n is None, then list all element counts.
+
+        >>> Counter('abracadabra').most_common(3)
+        [('a', 5), ('r', 2), ('b', 2)]
+
+        '''        
+        if n is None:
+            return sorted(self.iteritems(), key=itemgetter(1), reverse=True)
+        return nlargest(n, self.iteritems(), key=itemgetter(1))
+
+    def elements(self):
+        '''Iterator over elements repeating each as many times as its count.
+
+        >>> c = Counter('ABCABC')
+        >>> sorted(c.elements())
+        ['A', 'A', 'B', 'B', 'C', 'C']
+
+        If an element's count has been set to zero or is a negative number,
+        elements() will ignore it.
+
+        '''
+        for elem, count in self.iteritems():
+            for _ in repeat(None, count):
+                yield elem
+
+    # Override dict methods where the meaning changes for Counter objects.
+
+    @classmethod
+    def fromkeys(cls, iterable, v=None):
+        raise NotImplementedError(
+            'Counter.fromkeys() is undefined.  Use Counter(iterable) instead.')
+
+    def update(self, iterable=None, **kwds):
+        '''Like dict.update() but add counts instead of replacing them.
+
+        Source can be an iterable, a dictionary, or another Counter instance.
+
+        >>> c = Counter('which')
+        >>> c.update('witch')           # add elements from another iterable
+        >>> d = Counter('watch')
+        >>> c.update(d)                 # add elements from another counter
+        >>> c['h']                      # four 'h' in which, witch, and watch
+        4
+
+        '''        
+        if iterable is not None:
+            if hasattr(iterable, 'iteritems'):
+                if self:
+                    self_get = self.get
+                    for elem, count in iterable.iteritems():
+                        self[elem] = self_get(elem, 0) + count
+                else:
+                    dict.update(self, iterable) # fast path when counter is empty
+            else:
+                self_get = self.get
+                for elem in iterable:
+                    self[elem] = self_get(elem, 0) + 1
+        if kwds:
+            self.update(kwds)
+
+    def copy(self):
+        'Like dict.copy() but returns a Counter instance instead of a dict.'
+        return Counter(self)
+
+    def __delitem__(self, elem):
+        'Like dict.__delitem__() but does not raise KeyError for missing values.'
+        if elem in self:
+            dict.__delitem__(self, elem)
+
+    def __repr__(self):
+        if not self:
+            return '%s()' % self.__class__.__name__
+        items = ', '.join(map('%r: %r'.__mod__, self.most_common()))
+        return '%s({%s})' % (self.__class__.__name__, items)
+
+    # Multiset-style mathematical operations discussed in:
+    #       Knuth TAOCP Volume II section 4.6.3 exercise 19
+    #       and at http://en.wikipedia.org/wiki/Multiset
+    #
+    # Outputs guaranteed to only include positive counts.
+    #
+    # To strip negative and zero counts, add-in an empty counter:
+    #       c += Counter()
+
+    def __add__(self, other):
+        '''Add counts from two counters.
+
+        >>> Counter('abbb') + Counter('bcc')
+        Counter({'b': 4, 'c': 2, 'a': 1})
+
+
+        '''
+        if not isinstance(other, Counter):
+            return NotImplemented
+        result = Counter()
+        for elem in set(self) | set(other):
+            newcount = self[elem] + other[elem]
+            if newcount > 0:
+                result[elem] = newcount
+        return result
+
+    def __sub__(self, other):
+        ''' Subtract count, but keep only results with positive counts.
+
+        >>> Counter('abbbc') - Counter('bccd')
+        Counter({'b': 2, 'a': 1})
+
+        '''
+        if not isinstance(other, Counter):
+            return NotImplemented
+        result = Counter()
+        for elem in set(self) | set(other):
+            newcount = self[elem] - other[elem]
+            if newcount > 0:
+                result[elem] = newcount
+        return result
+
+    def __or__(self, other):
+        '''Union is the maximum of value in either of the input counters.
+
+        >>> Counter('abbb') | Counter('bcc')
+        Counter({'b': 3, 'c': 2, 'a': 1})
+
+        '''
+        if not isinstance(other, Counter):
+            return NotImplemented
+        _max = max
+        result = Counter()
+        for elem in set(self) | set(other):
+            newcount = _max(self[elem], other[elem])
+            if newcount > 0:
+                result[elem] = newcount
+        return result
+
+    def __and__(self, other):
+        ''' Intersection is the minimum of corresponding counts.
+
+        >>> Counter('abbb') & Counter('bcc')
+        Counter({'b': 1})
+
+        '''
+        if not isinstance(other, Counter):
+            return NotImplemented
+        _min = min
+        result = Counter()
+        if len(self) < len(other):
+            self, other = other, self
+        for elem in ifilter(self.__contains__, other):
+            newcount = _min(self[elem], other[elem])
+            if newcount > 0:
+                result[elem] = newcount
+        return result
+
+
+if __name__ == '__main__':
+    import doctest
+    print doctest.testmod()
+

src/obitools/ecopcr/taxonomy.py

@@ -7,7 +7,11 @@ from obitools.ecopcr import EcoPCRDBFile
 from obitools.utils import universalOpen
 from obitools.utils import ColumnFile
 import math
+try:
     from collections import Counter
+except ImportError:
+    from obitools.collections import Counter
+
 
 class Taxonomy(object):
     def __init__(self):

src/obitools/sample.py

@@ -4,7 +4,11 @@ Created on 31 oct. 2009
 @author: coissac
 '''
 from random import randrange, sample
-from obitools.utils import Counter
+try:
+    from collections import Counter
+except ImportError:
+    from obitools.collections import Counter
+
 
 def lookfor(x,cumsum):
     lmax=len(cumsum)

src/obitools/utils/__init__.py

@@ -15,7 +15,10 @@ import os.path
 from _utils import FakeFile
 from _utils import progressBar
 
+try:
     from collections import Counter
+except ImportError:
+    from obitools.collections import Counter
 
 
 class FileFormatError(Exception):