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#!/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 random
import tempfile
import unittest
from string import ascii_lowercase
from io import BytesIO
import warnings
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonDeprecationWarning)
warnings.simplefilter('ignore', RuntimeWarning) # for the trie module
try:
from Bio import trie
from Bio import triefind
except ImportError:
import os
from Bio import MissingPythonDependencyError
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 MissingPythonDependencyError(message)
class TestTrie(unittest.TestCase):
def test_get_set(self):
trieobj = trie.trie()
trieobj["hello world"] = "s1"
trieobj["bye"] = "s2"
trieobj["hell sucks"] = "s3"
trieobj["hebee"] = "s4"
self.assertEqual(trieobj["hello world"], "s1")
self.assertEqual(trieobj["bye"], "s2")
self.assertEqual(trieobj["hell sucks"], "s3")
self.assertEqual(trieobj["hebee"], "s4")
trieobj["blah"] = "s5"
self.assertEqual(trieobj["blah"], "s5")
self.assertEqual(trieobj.get("foobar"), None)
self.assertEqual(len(trieobj), 5)
trieobj["blah"] = "snew"
self.assertEqual(trieobj["blah"], "snew")
def test_prefix(self):
trieobj = trie.trie()
trieobj["hello"] = 5
trieobj["he"] = 7
trieobj["hej"] = 9
trieobj["foo"] = "bar"
k = sorted(trieobj.keys())
self.assertEqual(k, ["foo", "he", "hej", "hello"])
self.assertEqual(trieobj["hello"], 5)
self.assertEqual(trieobj.get("bye"), None)
self.assertIn("hello", trieobj)
self.assertIn("he", trieobj)
self.assertFalse("bye" in trieobj)
self.assertTrue(trieobj.has_prefix("h"))
self.assertTrue(trieobj.has_prefix("hel"))
self.assertFalse(trieobj.has_prefix("foa"))
self.assertFalse(trieobj.has_prefix("hello world"))
self.assertEqual(len(trieobj), 4)
k = sorted(trieobj.with_prefix("he"))
self.assertEqual(k, ["he", "hej", "hello"])
k = trieobj.with_prefix("l")
self.assertEqual(k, [])
k = trieobj.with_prefix("hej")
self.assertEqual(k, ["hej"])
k = trieobj.with_prefix("hejk")
self.assertEqual(k, [])
def test_save(self):
trieobj = trie.trie()
trieobj["foo"] = 1
k = list(trieobj.keys())
self.assertEqual(k, ["foo"])
v = list(trieobj.values())
self.assertEqual(v, [1])
self.assertEqual(trieobj.get("bar", 99), 99)
trieobj["hello"] = '55a'
self.assertEqual(trieobj.get_approximate("foo", 0), [("foo", 1, 0)])
self.assertEqual(trieobj.get_approximate("foo", 1), [("foo", 1, 0)])
self.assertEqual(trieobj.get_approximate("foa", 0), [])
self.assertEqual(trieobj.get_approximate("foa", 1), [("foo", 1, 1)])
x = sorted(trieobj.get_approximate("foa", 2))
self.assertEqual(x, [("foo", 1, 1), ("foo", 1, 2), ("foo", 1, 2)])
# foo foo- foo-
# foa f-oa fo-a
# mismatch a->o
# insertion after f, deletion of o
# insertion after o, deletion of o
x = trieobj.get_approximate("foo", 4)
y = {}
for z in x:
y[z] = y.get(z, 0) + 1
x = sorted(y.items())
self.assertEqual(x, [(('foo', 1, 0), 1), (('hello', '55a', 4), 6)])
h = BytesIO()
trie.save(h, trieobj)
h.seek(0)
trieobj = trie.load(h)
k = list(trieobj.keys())
self.assertIn("foo", k)
self.assertIn("hello", k)
self.assertEqual(repr(trieobj["foo"]), '1')
self.assertEqual(repr(trieobj["hello"]), "'55a'")
def test_get_approximate(self):
# Found bug, doesn't handle insertions and deletions at end properly.
trieobj = trie.trie()
trieobj["hello"] = 1
self.assertEqual(trieobj.get_approximate('he', 2), [])
self.assertEqual(trieobj.get_approximate('he', 3), [('hello', 1, 3)])
self.assertEqual(trieobj.get_approximate('hello me!', 3), [])
self.assertEqual(trieobj.get_approximate('hello me!', 4), [('hello', 1, 4)])
self.assertEqual(trieobj.get_approximate('hello me!', 5), [('hello', 1, 4)])
def test_with_prefix(self):
trieobj = trie.trie()
s = "BANANA"
for i in range(len(s)): # insert all suffixes into trie
trieobj[s[i:]] = i
self.assertEqual(trieobj[s[i:]], i)
self.assertEqual(set(trieobj.values()), set(range(6)))
self.assertEqual(set(['A', 'ANA', 'ANANA', 'BANANA', 'NA', 'NANA']),
set(trieobj.keys()))
self.assertEqual(set(['NA', 'NANA']),
set(trieobj.with_prefix("N")))
self.assertEqual(set(['NA', 'NANA']),
set(trieobj.with_prefix("NA")))
self.assertEqual(set(['A', 'ANA', 'ANANA']),
set(trieobj.with_prefix("A")))
self.assertEqual(set(['ANA', 'ANANA']),
set(trieobj.with_prefix("AN")))
def test_large_save_load(self):
"""Generate random key/val pairs in three length categories.
100 items in each category. Insert them into a trie and into a reference dict.
Write the trie to a temp file and read it back, verify that trie entries match
the reference dict.
"""
cmp_dict = {}
trieobj = trie.trie()
self.assertEqual(trieobj.get("foobar"), None)
for max_str_len in [100, 1000, 10000]:
cmp_dict = {}
for i in range(1000):
key = ''.join([random.choice(ascii_lowercase) for _ in range(max_str_len)])
val = ''.join([random.choice(ascii_lowercase) for _ in range(max_str_len)])
trieobj[key] = val
cmp_dict[key] = val
for key in cmp_dict:
self.assertEqual(trieobj[key], cmp_dict[key])
with tempfile.TemporaryFile(mode='w+b') as f:
trie.save(f, trieobj)
f.seek(0)
trieobj = trie.load(f)
for key in cmp_dict:
self.assertEqual(trieobj[key], cmp_dict[key])
class TestTrieFind(unittest.TestCase):
def test_find(self):
trieobj = trie.trie()
trieobj["hello"] = 5
trieobj["he"] = 7
trieobj["hej"] = 9
trieobj["foo"] = "bar"
trieobj["wor"] = "ld"
self.assertEqual(triefind.match("hello world!", trieobj), "hello")
k = sorted(triefind.match_all("hello world!", trieobj))
self.assertEqual(k, ["he", "hello"])
k = sorted(triefind.find("hello world!", trieobj))
self.assertEqual(k, [("he", 0, 2), ("hello", 0, 5), ("wor", 6, 9)])
k = sorted(triefind.find_words("hello world!", trieobj))
self.assertEqual(k, [("hello", 0, 5)])
trieobj["world"] = "full"
k = sorted(triefind.find("hello world!", trieobj))
self.assertEqual(k, [("he", 0, 2), ("hello", 0, 5), ("wor", 6, 9), ("world", 6, 11)])
k = sorted(triefind.find_words("hello world!", trieobj))
self.assertEqual(k, [("hello", 0, 5), ("world", 6, 11)])
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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