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
129
130
131
132
133
134
135
136
137
138
139
140
141
|
Description: Switch to pytest from nose since the latter is now deprecated
Author: Mohammed Bilal <mdbilal@disroot.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1018506
Forwarded: https://github.com/openvax/gtfparse/issues/29
Last-Update: 2022-12-04
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/test/test_expand_attributes.py
+++ b/test/test_expand_attributes.py
@@ -1,5 +1,4 @@
from gtfparse import expand_attribute_strings
-from nose.tools import eq_
def test_attributes_in_quotes():
attributes = [
@@ -7,10 +6,10 @@
"gene_id \"ENSG002\"; tag \"wolfpuppy\"; version \"2\";"
]
parsed_dict = expand_attribute_strings(attributes)
- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"])
- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
- eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
- eq_(parsed_dict["version"], ["1", "2"])
+ assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
+ assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
+ assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
+ assert parsed_dict["version"] == ["1", "2"]
def test_attributes_without_quotes():
@@ -19,10 +18,10 @@
"gene_id ENSG002; tag wolfpuppy; version 2"
]
parsed_dict = expand_attribute_strings(attributes)
- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"])
- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
- eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
- eq_(parsed_dict["version"], ["1", "2"])
+ assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
+ assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
+ assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
+ assert parsed_dict["version"] == ["1", "2"]
def test_optional_attributes():
@@ -32,6 +31,6 @@
"gene_id ENSG003; sometimes-present wolfpuppy;",
]
parsed_dict = expand_attribute_strings(attributes)
- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "sometimes-present"])
- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002", "ENSG003"])
- eq_(parsed_dict["sometimes-present"], ["bogotron", "", "wolfpuppy"])
+ assert list(sorted(parsed_dict.keys())) == ["gene_id", "sometimes-present"]
+ assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002", "ENSG003"]
+ assert parsed_dict["sometimes-present"] == ["bogotron", "", "wolfpuppy"]
--- a/test/test_multiple_values_for_tag_attribute.py
+++ b/test/test_multiple_values_for_tag_attribute.py
@@ -1,6 +1,5 @@
from six import StringIO
from gtfparse import parse_gtf_and_expand_attributes
-from nose.tools import eq_
# failing example from https://github.com/openvax/gtfparse/issues/2
GTF_TEXT = (
@@ -15,18 +14,18 @@
def test_parse_tag_attributes():
parsed = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT))
tag_column = parsed["tag"]
- eq_(len(tag_column), 1)
+ assert len(tag_column) == 1
tags = tag_column[0]
- eq_(tags, 'cds_end_NF,mRNA_end_NF')
+ assert tags == 'cds_end_NF,mRNA_end_NF'
def test_parse_tag_attributes_with_usecols():
parsed = parse_gtf_and_expand_attributes(
StringIO(GTF_TEXT),
restrict_attribute_columns=["tag"])
tag_column = parsed["tag"]
- eq_(len(tag_column), 1)
+ assert len(tag_column) == 1
tags = tag_column[0]
- eq_(tags, 'cds_end_NF,mRNA_end_NF')
+ assert tags == 'cds_end_NF,mRNA_end_NF'
def test_parse_tag_attributes_with_usecols_other_column():
parsed = parse_gtf_and_expand_attributes(
--- a/test/test_parse_gtf_lines.py
+++ b/test/test_parse_gtf_lines.py
@@ -1,5 +1,4 @@
import numpy as np
-from nose.tools import eq_, assert_raises
from gtfparse import (
parse_gtf,
parse_gtf_and_expand_attributes,
@@ -7,6 +6,7 @@
ParsingError
)
from six import StringIO
+from pytest import raises as assert_raises
gtf_text = """
# sample GTF data copied from:
@@ -28,27 +28,27 @@
"transcript_source",
]
# convert to list since Py3's dictionary keys are a distinct collection type
- eq_(list(parsed_dict.keys()), expected_columns)
- eq_(list(parsed_dict["seqname"]), ["1", "1"])
+ assert list(parsed_dict.keys()) == expected_columns
+ assert list(parsed_dict["seqname"]) == ["1", "1"]
# convert to list for comparison since numerical columns may be NumPy arrays
- eq_(list(parsed_dict["start"]), [11869, 11869])
- eq_(list(parsed_dict["end"]), [14409, 14409])
+ assert list(parsed_dict["start"]) == [11869, 11869]
+ assert list(parsed_dict["end"]) == [14409, 14409]
# can't compare NaN with equality
scores = list(parsed_dict["score"])
assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
- eq_(list(parsed_dict["gene_id"]), ["ENSG00000223972", "ENSG00000223972"])
- eq_(list(parsed_dict["transcript_id"]), ["", "ENST00000456328"])
+ assert list(parsed_dict["gene_id"]) == ["ENSG00000223972", "ENSG00000223972"]
+ assert list(parsed_dict["transcript_id"]) == ["", "ENST00000456328"]
def test_parse_gtf_lines_without_expand_attributes():
parsed_dict = parse_gtf(StringIO(gtf_text))
# convert to list since Py3's dictionary keys are a distinct collection type
- eq_(list(parsed_dict.keys()), REQUIRED_COLUMNS)
- eq_(list(parsed_dict["seqname"]), ["1", "1"])
+ assert list(parsed_dict.keys()) == REQUIRED_COLUMNS
+ assert list(parsed_dict["seqname"]) == ["1", "1"]
# convert to list for comparison since numerical columns may be NumPy arrays
- eq_(list(parsed_dict["start"]), [11869, 11869])
- eq_(list(parsed_dict["end"]), [14409, 14409])
+ assert list(parsed_dict["start"]) == [11869, 11869]
+ assert list(parsed_dict["end"]) == [14409, 14409]
# can't compare NaN with equality
scores = list(parsed_dict["score"])
assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
|
