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
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
"""gn3.computations.rust_correlation unittests"""
import json
import os
import pytest
from gn3.computations.rust_correlation import generate_json_file
from gn3.computations.rust_correlation import generate_input_files
from gn3.computations.rust_correlation import get_samples
from gn3.computations.rust_correlation import parse_correlation_output
@pytest.mark.unit_test
def test_generate_input():
"""test generating text files"""
test_dataset = [
"14_at,12.1,14.1,None",
"15_at,12.2,14.1,None",
"17_at,12.1,14.1,11.4"
]
(_tmp_dir, tmp_file) = generate_input_files(test_dataset,
output_dir="/tmp")
with open(tmp_file, "r", encoding="utf-8") as file_reader:
test_results = [line.rstrip() for line in file_reader]
os.remove(tmp_file)
assert test_results == test_dataset
# @pytest.mark.unit_test
def test_json_file():
"""test for generating json files """
tmp_file = generate_json_file(tmp_dir="/tmp/correlation",
tmp_file="/data.txt",
method="pearson",
x_vals="12.1,11.3,16.5,7.5,3.2",
delimiter=",")
with open(tmp_file, "r+", encoding="utf-8") as file_reader:
results = json.load(file_reader)
assert results == {
"method": "pearson",
"file_path": "/data.txt",
"x_vals": "12.1,11.3,16.5,7.5,3.2",
"file_delimiter": ","}
@pytest.mark.unit_test
def test_parse_results():
"""test for parsing file results"""
raw_data = [
["63.62", "0.97", "0.00"],
["19", "-0.96", "0.22"],
["77.92", "-0.94", "0.31"],
["84.04", "0.94", "0.11"],
["23", "-0.91", "0.11"]
]
raw_dict = [{trait: {
"num_overlap": 00,
"p_value": p_val}} for (trait, corr_coeff, p_val) in raw_data]
assert (parse_correlation_output(
"tests/unit/computations/data/correlation/sorted_results.txt",
len(raw_data))
== raw_dict)
@pytest.mark.unit_test
def test_get_samples_no_excluded():
"""test for getting sample data"""
al_samples = {
"BXD": "12.1",
"BXD3": "16.1",
"BXD4": " x",
"BXD6": "1.1",
"BXD5": "1.37",
"BXD11": "1.91",
"BXD31": "1.1"
}
base = [
"BXD",
"BXD4",
"BXD7",
"BXD31"
]
assert get_samples(all_samples=al_samples,
base_samples=base,
excluded=[]) == {
"BXD": 12.1,
"BXD31": 1.1
}
@pytest.mark.unit_test
def test_get_samples():
"""test for getting samples with exluded"""
al_samples = {
"BXD": "12.1",
"BXD3": "16.1",
"BXD4": " x",
"BXD5": "1.1",
"BXD6": "1.37",
"BXD11": "1.91",
"BXD31": "1.1"
}
assert get_samples(all_samples=al_samples,
base_samples=["BXD", "BXD4", "BXD5", "BXD6",
"BXD11"
], excluded=["BXD", "BXD11"]), {
"BXD5": 1.1,
"BXD6": 1.37
}
|