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
|
import shutil
from subprocess import PIPE, Popen
from typing import List, TextIO
import pytest
from . import data_stream
def _exec(
args: List[str], outputtext: List[str], returncode: int = 0, stdin: TextIO = None
) -> None:
if not stdin:
stdin = data_stream("cap.fa")
args = ["weblogo"] + args
p = Popen(args, stdin=stdin, stdout=PIPE, stderr=PIPE)
(out, err) = p.communicate()
if returncode == 0 and p.returncode > 0:
print(err)
assert returncode == p.returncode
if returncode == 0:
assert len(err) == 0
if outputtext:
outs = out.decode()
for item in outputtext:
assert item in outs
stdin.close()
def test_malformed_options() -> None:
_exec(["--notarealoption"], [], 2)
_exec(["extrajunk"], [], 2)
_exec(["-I"], [], 2)
def test_help_option() -> None:
_exec(["-h"], ["options"])
_exec(["--help"], ["options"])
# def test_version_option():
# _exec(['--version'], weblogo.__version__[0:5])
def test_default_build() -> None:
_exec([], ["%%Title: Sequence Logo:"])
# Format options
def test_width() -> None:
_exec(["-W", "1234"], ["/stack_width 1234"])
_exec(["--stack-width", "1234"], ["/stack_width 1234"])
def test_height() -> None:
_exec(["-W", "1000"], ["/stack_height 5000"])
_exec(["-W", "1000", "--aspect-ratio", "2"], ["/stack_height 2000"])
def test_stacks_per_line() -> None:
_exec(["-n", "7"], ["/stacks_per_line 7 def"])
_exec(["--stacks-per-line", "7"], ["/stacks_per_line 7 def"])
def test_title() -> None:
_exec(
["-t", "3456"],
["/logo_title (3456) def", "/show_title True def"],
)
_exec(["-t", ""], ["/logo_title () def", "/show_title False def"])
_exec(
["--title", "3456"],
["/logo_title (3456) def", "/show_title True def"],
)
def test_annotate() -> None:
_exec(["--annotate", "1,2,3,4"], [], 2)
_exec(["--annotate", "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,,"], [])
def test_color() -> None:
_exec(["--color", "black", "AG", "Purine"], [])
_exec(["--color", "not_a_color", "AG", "Purine"], [], 2)
def test_reverse_complement() -> None:
_exec(["--complement"], [])
_exec(["--reverse"], [])
_exec(["--revcomp"], [])
def test_formats() -> None:
_exec(["--format", "eps"], [])
_exec(["--format", "png"], [])
_exec(["--format", "png_print"], [])
_exec(["--format", "pdf"], [])
_exec(["--format", "jpeg"], [])
_exec(["--format", "logodata"], [])
@pytest.mark.skipif(shutil.which("pdf2svg") is None, reason="requires pdf2svg")
def test_formats_svg() -> None:
_exec(["--format", "svg"], [])
|
