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
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
|
import tempfile
from gffutils import parser, create, feature, iterators, constants, helpers, exceptions
from gffutils import example_filename, create_db
from . import attr_test_cases
from textwrap import dedent
import pytest
TEST_FILENAMES = [
example_filename(i)
for i in [
"c_elegans_WS199_ann_gff.txt",
"ensembl_gtf.txt",
"hybrid1.gff3",
"ncbi_gff3.txt",
"c_elegans_WS199_dna_shortened.fa",
"F3-unique-3.v2.gff",
"jgi_gff2.txt",
"wormbase_gff2_alt.txt",
"c_elegans_WS199_shortened_gff.txt",
"glimmer_nokeyval.gff3",
"mouse_extra_comma.gff3",
"wormbase_gff2.txt",
]
]
def test_directives():
data = dedent(
"""
##directive1 example
. . . . . . . .
. . . . . . . .
. . . . . . . .
. . . . . . . .
"""
)
it = iterators.DataIterator(data, from_string=True)
assert it.directives == ["directive1 example"]
db = create_db(data, dbfn=":memory:", from_string=True, verbose=False)
assert db.directives == ["directive1 example"], db.directives
@pytest.mark.parametrize("item", attr_test_cases.attrs)
def test_attrs_OK(item):
"""
Given an attribute string and a dictionary of what you expect, test the
attribute splitting and reconstruction (invariant roundtrip).
There are some corner cases for the roundtrip invariance that don't work
(see attr_test_cases.py for details); `acceptable_reconstruction` handles
those.
"""
attr_str, attr_dict, acceptable_reconstruction = item
result, dialect = parser._split_keyvals(attr_str)
result = dict(result)
assert result == attr_dict, result
reconstructed = parser._reconstruct(result, dialect, keep_order=True)
if acceptable_reconstruction:
assert reconstructed == acceptable_reconstruction, reconstructed
else:
assert reconstructed == attr_str, reconstructed
def parser_smoke_test():
"""
Just confirm we can iterate completely through the test files....
"""
# Don't show the warnings for tests
import logging
parser.logger.setLevel(logging.CRITICAL)
for filename in TEST_FILENAMES:
p = iterators._FileIterator(filename)
for i in p:
continue
def test_empty_recontruct():
"""
reconstructing attributes with incomplete information returns empty string
"""
assert parser._reconstruct(None, constants.dialect) == ""
with pytest.raises(exceptions.AttributeStringError):
parser._reconstruct(dict(ID="asdf"), None)
with pytest.raises(exceptions.AttributeStringError):
parser._reconstruct(None, None)
def test_empty_split_keyvals():
attrs, dialect = parser._split_keyvals(keyval_str=None)
assert attrs == feature.dict_class()
assert dialect == constants.dialect
def test_repeated_keys_conflict():
"""
if dialect says repeated keys, but len(vals) > 1, then the keys are not
actually repeated....
"""
#
# This is now only checked when infer_dialect is True -- and is disabled
# when a dialect is provided
#
# dialect = constants.dialect.copy()
# dialect['repeated keys'] = True
# assert_raises(exceptions.AttributeStringError, parser._split_keyvals, "Parent=1,2,3", dialect)
def test_parser_from_string():
# DEPRECATED
#
# _StringIterator has been removed and is instead handled by DataIterator
# creating a temp file and returning a _FileIterator.
return True
def test_valid_line_count():
p = iterators._FileIterator(example_filename("ncbi_gff3.txt"))
assert len(list(p)) == 17
p = iterators._FileIterator(example_filename("hybrid1.gff3"))
assert len(list(p)) == 6
p = iterators._FileIterator(example_filename("FBgn0031208.gff"))
assert len(list(p)) == 27
def test_inconsistent_dialect():
"""
The second feature does not have a trailing semicolon (wormbase_gff2_alt is
like this). But since the first feature does, that's what the db's dialect
is set to, which can cause errors when parsing attributes.
"""
db = create.create_db(
"""
chr1 . gene 1 100 . + . gene_id "gene1";
chr1 . mRNA 1 100 . + . transcript_id "mRNA1"
""",
":memory:",
from_string=True,
)
items = list(db.all_features())
print(items[0])
# before, was ['"mRNA1'] -- note extra "
assert items[1].attributes["transcript_id"] == ["mRNA1"], items[1].attributes[
"transcript_id"
]
def test_attributes():
s = "chr2L FlyBase mRNA 7529 9484 . + . ID=FBtr0300690;Name=CG11023-RC;Parent=FBgn0031208;"
f = feature.feature_from_line(s)
f.keep_order = True
assert str(f) == s, str(f)
|
