boolbins/test.py at master · BlishLab/boolbins · GitHub

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
#!/usr/bin/env python

import boolbins
import unittest
import os.path


SIMPLE_OUT = """
,tests/first9.csv
[],0.7777777777777778
beads,0.2222222222222222
"""
SIMPLE_OUT_WITH_LIMIT = """
,tests/first9.csv
[],0.3333333333333333
beads,0.6666666666666666
"""
MULTIPLE_OUT = """
,tests/first9.csv
[],0.5555555555555556
HLADR,0.2222222222222222
beads,0.1111111111111111
HLADR beads,0.1111111111111111
"""
MULTIPLE_FILES_OUT = """
,tests/first5.csv,tests/first9.csv
[],0.6,0.5555555555555556
beads,0,0.1111111111111111
HLADR,0.2,0.2222222222222222
HLADR beads,0.2,0.1111111111111111
"""
DIVERSITY_FILE_OUT = """
File,Diversity
tests/first5.csv,2.272727272727273
tests/first9.csv,2.6129032258064515
"""


class TestBasic(unittest.TestCase):
    output_file = "tests/output.csv"
    diversity_file = "tests/diversity.csv"
    def cleanup_files(self):
        for f in [self.output_file, self.diversity_file]:
            if os.path.exists(f):
                os.remove(f)

    def setUp(self):
        self.cleanup_files()

    def tearDown(self):
        self.cleanup_files()

    def test_one_threshold(self):
        boolbins.run("tests/thresholds_simple.csv", ["tests/first9.csv"], self.output_file, 0, '')
        self.assertEqual(open(self.output_file, "rU").read().strip(), SIMPLE_OUT.strip())

    def test_one_threshold_with_limit(self):
        boolbins.run("tests/thresholds_simple.csv", ["tests/first9.csv"], self.output_file, 3, '')
        self.assertEqual(open(self.output_file, "rU").read().strip(), SIMPLE_OUT_WITH_LIMIT.strip())

    def test_multiple_thresholds(self):
        boolbins.run("tests/thresholds_multiple.csv", ["tests/first9.csv"], self.output_file, 0, '')
        self.assertEqual(open(self.output_file, "rU").read().strip(), MULTIPLE_OUT.strip())

    def test_multiple_thresholds_multiple_files(self):
        boolbins.run("tests/thresholds_multiple.csv", ["tests/first9.csv", "tests/first5.csv"], self.output_file, 0, '')
        self.assertEqual(open(self.output_file, "rU").read().strip(), MULTIPLE_FILES_OUT.strip())

    def test_diversity_scores(self):
        boolbins.run("tests/thresholds_multiple.csv", ["tests/first9.csv", "tests/first5.csv"], self.output_file, 0, self.diversity_file)
        self.assertEqual(open(self.diversity_file, "rU").read().strip(), DIVERSITY_FILE_OUT.strip())