Package Bio :: Module listfns
[hide private]
[frames] | no frames]

Source Code for Module Bio.listfns

  1  # Copyright 2000 by Jeffrey Chang.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6  """This provides useful general functions for working with lists (OBSOLETE). 
  7   
  8  This module and its C code equivalent are considered to be obsolete, and 
  9  are likely to be deprecated in a future release of Biopython, before being 
 10  removed.  Please get in touch via the mailing list if this will affect you. 
 11  Many of these functions can be avoided using the python set object. 
 12   
 13  Functions: 
 14  asdict        Make the list into a dictionary (for fast testing of membership). 
 15  items         Get one of each item in a list. 
 16  count         Count the number of times each item appears. 
 17  contents      Calculate percentage each item appears in a list. 
 18  itemindex     Make an index of the items in the list. 
 19  intersection  Get the items in common between 2 lists. 
 20  difference    Get the items in 1 list, but not the other. 
 21  indexesof     Get a list of the indexes of some items in a list. 
 22  take          Take some items from a list. 
 23   
 24  """ 
 25   
26 -def asdict(l):
27 """asdict(l) -> dictionary 28 29 Return a dictionary where the keys are the items in the list, with 30 arbitrary values. This is useful for quick testing of membership. 31 32 """ 33 return count(l)
34
35 -def items(l):
36 """items(l) -> list of items 37 38 Generate a list of one of each item in l. The items are returned 39 in arbitrary order. 40 41 """ 42 try: 43 return asdict(l).keys() 44 except TypeError, x: 45 if str(x).find("unhashable") == -1: 46 raise 47 # asdict failed because l is unhashable. Back up to a naive 48 # implementation. 49 l = l[:] 50 l.sort() 51 i = 0 52 while i < len(l)-1: 53 if l[i] == l[i+1]: 54 del l[i] 55 else: 56 i += 1 57 return l
58
59 -def count(items):
60 """count(items) -> dict of counts of each item 61 62 Count the number of times each item appears in a list of data. 63 64 """ 65 c = {} 66 for i in items: 67 c[i] = c.get(i, 0) + 1 68 return c
69
70 -def contents(items):
71 """contents(items) -> dict of item:percentage 72 73 Summarize the contents of the list in terms of the percentages of each 74 item. For example, if an item appears 3 times in a list with 10 items, 75 it is in 0.3 of the list. 76 77 """ 78 counts = count(items) 79 l = float(len(items)) 80 contents = {} 81 for i, c in counts.items(): 82 contents[i] = c / l 83 return contents
84
85 -def intersection(l1, l2):
86 """intersection(l1, l2) -> list of common items 87 88 Return a list of the items in both l1 and l2. The list is in 89 arbitrary order. 90 91 """ 92 inter = [] 93 words1 = count(l1) 94 for w in l2: 95 if words1.has_key(w): 96 inter.append(w) 97 del words1[w] # don't add the same word twice 98 return inter
99
100 -def difference(l1, l2):
101 """difference(l1, l2) -> list of items in l1, but not l2 102 103 Return a list of the items in l1, but not l2. The list is in 104 arbitrary order. 105 106 """ 107 diff = [] 108 words2 = count(l2) 109 for w in l1: 110 if not words2.has_key(w): 111 diff.append(w) 112 words2[w] = 1 # don't add the same word twice 113 return diff
114
115 -def itemindex(l):
116 """itemindex(l) -> dict of item : index of item 117 118 Make an index of the items in the list. The dictionary contains 119 the items in the list as the keys, and the index of the first 120 occurrence of the item as the value. 121 122 """ 123 dict = {} 124 for i in range(len(l)): 125 if not dict.has_key(l[i]): 126 dict[l[i]] = i 127 return dict
128
129 -def indexesof(l, fn, opposite=0):
130 """indexesof(l, fn) -> list of indexes 131 132 Return a list of indexes i where fn(l[i]) is true. 133 134 """ 135 indexes = [] 136 for i in range(len(l)): 137 f = fn(l[i]) 138 if (not opposite and f) or (opposite and not f): 139 indexes.append(i) 140 return indexes
141
142 -def take(l, indexes):
143 """take(l, indexes) -> list of just the indexes from l""" 144 items = [] 145 for i in indexes: 146 items.append(l[i]) 147 return items
148
149 -def take_byfn(l, fn, opposite=0):
150 indexes = indexesof(l, fn, opposite=opposite) 151 return take(l, indexes)
152 153 # Try and load C implementations of functions. If I can't, 154 # then just ignore and use the pure python implementations. 155 try: 156 from clistfns import * 157 except ImportError: 158 pass 159