1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import StringIO
from operator import truth
try:
from Bio import trie
except ImportError:
import os
from Bio import MissingExternalDependencyError
if os.name=="java":
message = "Not available on Jython, Bio.trie requires compiled C code."
else:
message = "Could not import Bio.trie, check C code was compiled."
raise MissingExternalDependencyError(message)
trieobj = trie.trie()
trieobj["hello"] = 5
trieobj["he"] = 7
trieobj["hej"] = 9
trieobj["foo"] = "bar"
k = trieobj.keys()
k.sort()
print k # ["foo", "he", "hej", "hello"]
print trieobj["hello"] # 5
print trieobj.get("bye") # None
print trieobj.has_key("hello") # 1
print trieobj.has_key("he") # 1
print trieobj.has_key("bye") # 0
print trieobj.has_prefix("h") # 1
print trieobj.has_prefix("hel") # 1
print trieobj.has_prefix("foa") # 0
print trieobj.has_prefix("hello world") # 0
print len(trieobj) # 4
k = trieobj.with_prefix("he")
k.sort()
print k # ["he", "hej", "hello"]
k = trieobj.with_prefix("l")
k.sort()
print k # []
k = trieobj.with_prefix("hej")
k.sort()
print k # ["hej"]
k = trieobj.with_prefix("hejk")
k.sort()
print k # []
trieobj2 = trie.trie()
trieobj2["foo"] = 1
k = trieobj2.keys()
k.sort()
print k # ["foo"]
v = trieobj2.values()
v.sort()
print v # [1]
print trieobj2.get("bar", 99) # 99
trieobj2["hello"] = '55a'
print trieobj2.get_approximate("foo", 0) # [("foo", 1, 0)]
print trieobj2.get_approximate("foo", 1) # [("foo", 1, 0)]
print trieobj2.get_approximate("foa", 0) # []
print trieobj2.get_approximate("foa", 1) # [("foo", 1, 1)]
x = trieobj2.get_approximate("foa", 2)
print "found %d matches" % len(x) # 3
x.sort()
print x # [("foo", 1, 1), ("foo", 1, 2), ("foo", 1, 2)]
# foo foo- foo-
# foa f-oa fo-a
#import sys; sys.exit(0)
# mismatch a->o
# insertion after f, deletion of o
# insertion after o, deletion of o
x = trieobj2.get_approximate("foo", 4)
y = {}
for z in x:
y[z] = y.get(z, 0) + 1
x = y.items()
x.sort()
print x # [(('foo', 1, 0), 1), (('hello', '55a', 4), 6)]
h = StringIO.StringIO()
trie.save(h, trieobj2)
h.seek(0)
trieobj3 = trie.load(h)
k = trieobj3.keys()
k.sort()
for m in k: # foo 1
print m, repr(trieobj3[m]) # hello '55a'
# Found bug, doesn't handle insertions and deletions at end properly.
trieobj = trie.trie()
trieobj["hello"] = 1
print trieobj.get_approximate('he', 2) # []
print trieobj.get_approximate('he', 3) # [('hello', 1, 3)]
print trieobj.get_approximate('hello me!', 3) # []
print trieobj.get_approximate('hello me!', 4) # [('hello', 1, 4)]
print trieobj.get_approximate('hello me!', 5) # [('hello', 1, 4)]
|
