test_triefind.py

#!/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)


from Bio import triefind

trieobj = trie.trie()

trieobj["hello"] = 5
trieobj["he"] = 7
trieobj["hej"] = 9
trieobj["foo"] = "bar"
trieobj["wor"] = "ld"

print triefind.match("hello world!", trieobj)    # "hello"
k = triefind.match_all("hello world!", trieobj)
k.sort()
print k     # ["he", "hello"]

k = triefind.find("hello world!", trieobj)
k.sort()
print k     # [("he", 0, 2), ("hello", 0, 5), ("wor", 6, 9)]

k = triefind.find_words("hello world!", trieobj)
k.sort()
print k     # [("hello", 0, 5)]

trieobj["world"] = "full"
k = triefind.find("hello world!", trieobj)
k.sort()
print k     # [("he", 0, 2), ("hello", 0, 5), ("wor", 6, 9), ("world", 6, 11)]

k = triefind.find_words("hello world!", trieobj)
k.sort()
print k     # [("hello", 0, 5), ("world", 6, 11)]