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Metagenomics
metagenedb
Commits
eff3e6ce
Commit
eff3e6ce
authored
Dec 09, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
remove end line
parent
b3c47f2f
Changes
2
Hide whitespace changes
Inline
Side-by-side
backend/metagenedb/common/utils/parsers/eggnog.py
View file @
eff3e6ce
...
...
@@ -15,7 +15,7 @@ class EggNogAnnotationLineParser(object):
return
{
'functional_category'
:
elements
[
2
],
'function_id'
:
elements
[
1
],
'name'
:
elements
[
3
],
'name'
:
elements
[
3
]
.
rstrip
()
,
}
except
Exception
:
_LOGGER
.
error
(
f
"Could not parse:
{
line
.
rstrip
()
}
. Are you sure it comes from eggnog annotations.tsv?"
)
...
...
backend/metagenedb/common/utils/parsers/test_eggnog.py
View file @
eff3e6ce
...
...
@@ -5,8 +5,8 @@ from metagenedb.common.utils.parsers import EggNogAnnotationLineParser
class
TestEggNogAnnotationLineParser
(
TestCase
):
def
test_
ko_lis
t
(
self
):
ko_line
=
"1
\t
28H54
\t
K
\t
translational termination"
def
test_
get_dic
t
(
self
):
ko_line
=
"1
\t
28H54
\t
K
\t
translational termination
\n
"
expected_dict
=
{
'function_id'
:
"28H54"
,
'name'
:
"translational termination"
,
...
...
@@ -15,7 +15,17 @@ class TestEggNogAnnotationLineParser(TestCase):
test_dict
=
EggNogAnnotationLineParser
.
get_dict
(
ko_line
)
self
.
assertDictEqual
(
test_dict
,
expected_dict
)
def
test_ko_list_wrong_format
(
self
):
def
test_get_dict_no_name
(
self
):
ko_line
=
"1
\t
28H50
\t
S
\t\n
"
expected_dict
=
{
'function_id'
:
"28H50"
,
'name'
:
""
,
'functional_category'
:
"S"
}
test_dict
=
EggNogAnnotationLineParser
.
get_dict
(
ko_line
)
self
.
assertDictEqual
(
test_dict
,
expected_dict
)
def
test_get_dict_wrong_format
(
self
):
ko_line
=
"This is a wrong line format, with; information and tab"
with
self
.
assertRaises
(
Exception
)
as
context
:
# noqa
EggNogAnnotationLineParser
.
get_dict
(
ko_line
)
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