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
|
#!/usr/bin/env python
"""Tests for Genetic Algorithm Repair code.
This tests classes which are designed for repairing organisms after
mutation and crossover.
"""
# standard library
import unittest
# biopython
from Bio.Alphabet import Alphabet
from Bio.Seq import MutableSeq
# local stuff
from Bio.NeuralNetwork.Gene.Schema import Schema
from Bio.GA.Organism import Organism
from Bio.GA.Repair.Stabilizing import AmbiguousRepair
class TestAlphabet(Alphabet):
"""Simple test alphabet.
"""
alphabet_matches = {"1": "1",
"2": "2",
"3": "3",
"*": "123"}
letters = ["1", "2", "3", "*"]
def test_fitness(genome):
"""Simple class for calculating fitnesses.
"""
return 1
class AmbiguousRepairTest(unittest.TestCase):
"""Test for the ability to repair too many ambiguous genes in a genome.
"""
def setUp(self):
alphabet = TestAlphabet()
test_genome = MutableSeq("11*22*33*", alphabet)
self.organism = Organism(test_genome, test_fitness)
self.ambig_info = Schema(alphabet.alphabet_matches)
def test_single_repair(self):
"""Test repair of a single ambiguous position in a genome.
"""
repairer = AmbiguousRepair(self.ambig_info, 2)
for repair_attempt in range(5):
new_org = repairer.repair(self.organism)
new_genome_seq = new_org.genome.toseq()
assert new_genome_seq.count("*") == 2, \
"Did not repair genome, got %s" % str(new_genome_seq)
def test_multiple_repair(self):
"""Test repair of multiple ambiguous positions in a genome.
"""
repairer = AmbiguousRepair(self.ambig_info, 0)
for repair_attempt in range(5):
new_org = repairer.repair(self.organism)
new_genome_seq = new_org.genome.toseq()
assert new_genome_seq.count("*") == 0, \
"Did not repair genome, got %s" % str(new_genome_seq)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
