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vidjil
vidjil
Commits
7fab37d0
Commit
7fab37d0
authored
May 15, 2019
by
Thonier Florian
Browse files
test of clone, model and segmenter; update positons after fix of computeSegFeatureFromSeq fct
link to
#3488
parent
54200a08
Pipeline
#78281
passed with stages
in 5 minutes and 37 seconds
Changes
3
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
browser/test/QUnit/testFiles/clone_test.js
View file @
7fab37d0
...
...
@@ -311,7 +311,7 @@ QUnit.test("clone : feature defined by a nucleotide sequence", function(assert)
assert
.
deepEqual
(
c3
.
getSegStartStop
(
'
somefeature
'
),
null
,
"
start/stop positions are not present
"
)
c3
.
computeSegFeatureFromSeq
(
'
somefeature
'
)
assert
.
deepEqual
(
c3
.
getSegStartStop
(
'
somefeature
'
),
{
"
start
"
:
7
,
"
stop
"
:
1
3
},
"
start/stop positions, computed from sequence
"
)
assert
.
deepEqual
(
c3
.
getSegStartStop
(
'
somefeature
'
),
{
"
start
"
:
6
,
"
stop
"
:
1
2
},
"
start/stop positions, computed from sequence
"
)
assert
.
equal
(
c3
.
getSegLength
(
'
somefeature
'
),
7
,
"
length of the feature
"
);
});
...
...
browser/test/QUnit/testFiles/model_test.js
View file @
7fab37d0
...
...
@@ -349,8 +349,8 @@ QUnit.test("model: primer detection", function(assert) {
// primer found inside clones
assert
.
equal
(
typeof
m
.
clones
[
2
][
"
seg
"
][
"
primer5
"
],
"
undefined
"
,
"
Control neg primer 5 not in sequence
"
)
assert
.
equal
(
typeof
m
.
clones
[
2
][
"
seg
"
][
"
primer3
"
],
"
undefined
"
,
"
Control neg primer 3 not in sequence
"
)
assert
.
deepEqual
(
m
.
clones
[
3
][
"
seg
"
][
"
primer5
"
],
{
seq
:
"
GGAAGGCCCCACAGCG
"
,
start
:
1
,
stop
:
1
6
},
"
Found primer 5
"
)
assert
.
deepEqual
(
m
.
clones
[
3
][
"
seg
"
][
"
primer3
"
],
{
seq
:
"
AACTTCGCCTGGTAA
"
,
start
:
22
7
,
stop
:
24
1
},
"
Found primer 3
"
)
assert
.
deepEqual
(
m
.
clones
[
3
][
"
seg
"
][
"
primer5
"
],
{
seq
:
"
GGAAGGCCCCACAGCG
"
,
start
:
0
,
stop
:
1
5
},
"
Found primer 5
"
)
assert
.
deepEqual
(
m
.
clones
[
3
][
"
seg
"
][
"
primer3
"
],
{
seq
:
"
AACTTCGCCTGGTAA
"
,
start
:
22
6
,
stop
:
24
0
},
"
Found primer 3
"
)
m
.
cleanPreviousFeature
(
"
primer3
"
)
...
...
browser/test/QUnit/testFiles/segmenter_test.js
View file @
7fab37d0
...
...
@@ -111,8 +111,8 @@ QUnit.test("sequence", function(assert) {
assert
.
equal
(
h
.
stop
,
6
,
'
"f1" feature, stop
'
)
h
=
seq1
.
get_positionned_highlight
(
'
f2
'
,
''
)
assert
.
equal
(
h
.
start
,
1
5
,
'
"f2" feature, start
'
)
assert
.
equal
(
h
.
stop
,
20
,
'
"f2" feature, stop
'
)
assert
.
equal
(
h
.
start
,
1
4
,
'
"f2" feature, start
'
)
assert
.
equal
(
h
.
stop
,
19
,
'
"f2" feature, stop
'
)
segment
.
updateElemStyle
([
4
])
/* Will remove sequence 4 from the segmenter
* as it is not really selected
...
...
@@ -138,11 +138,11 @@ QUnit.test("segt", function (assert) {
assert
.
equal
(
m
.
clone
(
3
).
getSequence
(),
"
GGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGGCTGAAGGATTGGATCAAGACGTTTGCAAAAGGGACTAGGCTCATAGTAACTTCGCCTGGTAA
"
,
"
sequence
"
)
m
.
clone
(
3
).
addSegFeatureFromSeq
(
'
test_feature
'
,
'
CACCCAGGAGGTGGAGCTGGATATTGAGACT
'
);
f1
=
segment
.
sequence
[
3
].
get_positionned_highlight
(
'
test_feature
'
,
''
);
assert
.
equal
(
f1
.
start
,
9
4
,
"
feature start
"
);
assert
.
equal
(
f1
.
stop
,
12
4
,
"
feature stop
"
);
assert
.
equal
(
f1
.
start
,
9
3
,
"
feature start
"
);
assert
.
equal
(
f1
.
stop
,
12
3
,
"
feature stop
"
);
assert
.
equal
(
f1
.
seq
,
'
CACCCAGGAGGTGGAGCTGGATATTGAGACT
'
,
"
feature sequence
"
);
assert
.
equal
(
m
.
clone
(
3
).
getSegNtSequence
(
"
test_feature
"
),
"
CACCCAGGAGGTGGAGCTGGATATTGAGACT
"
,
"
feature sequence 3
"
);
assert
.
deepEqual
(
m
.
clone
(
3
).
getSegFeature
(
"
test_feature
"
),{
"
seq
"
:
"
CACCCAGGAGGTGGAGCTGGATATTGAGACT
"
,
"
start
"
:
9
4
,
"
stop
"
:
12
4
},
"
feature sequence 4
"
);
assert
.
deepEqual
(
m
.
clone
(
3
).
getSegFeature
(
"
test_feature
"
),{
"
seq
"
:
"
CACCCAGGAGGTGGAGCTGGATATTGAGACT
"
,
"
start
"
:
9
3
,
"
stop
"
:
12
3
},
"
feature sequence 4
"
);
// segment.sequence[3].computeAAseq()
// assert.equal(m.clone(3).getSegAASequence("cdr3"),"AKDILKSLKQQLATPNWFDP","feature sequence 2")
...
...
@@ -156,7 +156,7 @@ QUnit.test("segt", function (assert) {
var
h
=
segment
.
sequence
[
3
].
get_positionned_highlight
(
'
f1
'
,
''
);
assert
.
equal
(
h
.
start
,
-
1
,
"
start feature value
"
);
assert
.
equal
(
h
.
stop
,
-
1
,
"
stop feature value
"
);
assert
.
deepEqual
(
segment
.
sequence
[
3
].
get_positionned_highlight
(
"
test_feature
"
,
""
),{
"
color
"
:
""
,
"
css
"
:
"
highlight_seq
"
,
"
seq
"
:
"
CACCCAGGAGGTGGAGCTGGATATTGAGACT
"
,
"
start
"
:
9
4
,
"
stop
"
:
12
4
,
"
tooltip
"
:
""
},
"
test feature value
"
)
assert
.
deepEqual
(
segment
.
sequence
[
3
].
get_positionned_highlight
(
"
test_feature
"
,
""
),{
"
color
"
:
""
,
"
css
"
:
"
highlight_seq
"
,
"
seq
"
:
"
CACCCAGGAGGTGGAGCTGGATATTGAGACT
"
,
"
start
"
:
9
3
,
"
stop
"
:
12
3
,
"
tooltip
"
:
""
},
"
test feature value
"
)
assert
.
equal
(
m
.
clone
(
3
).
getSegLength
(
'
test_feature
'
),
31
,
"
feature length
"
);
m
.
unselectAll
();
assert
.
equal
(
segment
.
toFasta
(),
""
);
...
...
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