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minerva
core
Commits
8f75e96d
Commit
8f75e96d
authored
Jun 05, 2019
by
David Hoksza
Browse files
updated format for variants
parent
4de4b4ad
Pipeline
#10492
canceled with stage
in 10 minutes and 32 seconds
Changes
3
Pipelines
1
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frontend-js/package-lock.json
View file @
8f75e96d
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frontend-js/package.json
View file @
8f75e96d
...
...
@@ -37,7 +37,7 @@
"mkdirp"
:
"^0.5.1"
,
"mocha"
:
"^3.5.3"
,
"mock-local-storage"
:
"^1.1.8"
,
"molart"
:
"1.3.
1
"
,
"molart"
:
"1.3.
2
"
,
"stream-to-blob"
:
"^1.0.1"
,
"uglifyjs"
:
"^2.4.10"
},
...
...
frontend-js/src/main/js/map/structure/MolArt.js
View file @
8f75e96d
...
...
@@ -157,7 +157,7 @@ MolArt.prototype._activate = function (uniprotId) {
var
customDataSources
=
[];
for
(
var
i
=
0
;
i
<
variants
.
length
;
i
++
)
{
customDataSources
.
push
({
source
:
'
MINERVA
overlay <br/>
'
+
variants
[
i
].
overlayName
,
source
:
'
MINERVA
:
'
+
variants
[
i
].
overlayName
,
useExtension
:
false
,
data
:
constructVariantsData
(
sequence
,
variants
[
i
].
variants
)
});
...
...
@@ -251,15 +251,19 @@ var processGeneVariant = function(minervaVariant) {
// nonsynonymous_SNV TRIB3:NM_001301188:exon2:c.G82A:p.E28K,TRIB3:NM_001301190:exon2:c.G82A:p.E28K,TRIB3:NM_001301193:exon2:c.G82A:p.E28K,TRIB3:NM_001301196:exon2:c.G82A:p.E28K,TRIB3:NM_021158:exon2:c.G82A:p.E28K,TRIB3:NM_001301201:exon3:c.G163A:p.E55K
// frameshift insertion: LRRK2:NM_198578:exon1:c.151_152insCCTCCAAGTTATTTCAAGGCAAAAATATCCATGTGCCTCT:p.A51fs
// frameshift insertion: p.A51fsins
// frameshift insertion: NCOA3:NM_001174087:exon22:c.4171_4172insG:p.M1391fs,NCOA3:NM_001174088:exon22:c.4147_4148insG:p.M1383fs,NCOA3:NM_006534:exon22:c.4162_4163insG:p.M1388fs,NCOA3:NM_181659:exon22:c.4174_4175insG:p.M1392fs
// nonframeshift_insertion LRRK2:NM_198578:exon27:c.3777_3778insATTCCTCCT:p.E1259delinsEIPP
// nonframeshift_insertion p.E1259delinsEIPP
// nonframeshift_insertion SYNJ1:NM_001160306:exon28:c.3957_3958insAATACT:p.L1320delinsNTL,SYNJ1:NM_003895:exon32:c.4215_4216insAATACT:p.L1406delinsNTL
// frameshift_deletion LRRK2:NM_198578:exon17:c.2069_2070del:p.Q690fs
// frameshift_deletion ESF1:NM_001276380:exon14:c.2519_2520del:p.E840fs,ESF1:NM_016649:exon14:c.2519_2520del:p.E840fs
// frameshift_deletion p.Q690fsdel
// frameshift_deletion ESF1:NM_001276380:exon14:c.2519_2520del:p.E840fs,ESF1:NM_016649:exon14:c.2519_2520del:p.E840fsins
// nonframeshift_deletion LRRK2:NM_198578:exon9:c.1099_1101del:p.367_367del
// nonframeshift_deletion p.367_367del
// nonframeshift_deletion RRBP1:NM_004587:exon15:c.2022_2024del:p.674_675del,RRBP1:NM_001042576:exon16:c.2022_2024del:p.674_675del
...
...
@@ -270,35 +274,45 @@ var processGeneVariant = function(minervaVariant) {
for
(
var
i
=
0
;
i
<
sChange
.
length
;
i
++
)
{
var
aaChange
=
sChange
[
i
].
split
(
'
.
'
).
slice
(
-
1
)[
0
];
// LRRK2:NM_198578:exon1:c.T45C:p.T15T
var
variant
=
new
Variant
();
try
{
if
(
aaChange
.
endsWith
(
'
del
'
)
>
0
)
{
var
m
=
aaChange
.
match
(
/
(\d
+
)
_
(\d
+
)
/
);
[,
variant
.
posFrom
,
variant
.
posTo
]
=
m
;
variant
.
varType
=
'
Nonframeshift deletion
'
}
else
if
(
aaChange
.
endsWith
(
'
fs
'
)
||
aaChange
.
indexOf
(
'
delins
'
)
>=
0
)
{
var
m
=
aaChange
.
match
(
/
([
A-Z
])(\d
+
)
/
);
[
,
variant
.
aaFrom
,
variant
.
posFrom
]
=
m
;
if
(
change
.
indexOf
(
'
delins
'
)
>=
0
)
variant
.
varType
=
'
Nonframeshift insertion
'
;
else
if
(
change
.
indexOf
(
'
del
'
)
>=
0
)
variant
.
varType
=
'
Frameshift deletion
'
;
else
variant
.
varType
=
'
Frameshift insertion
'
;
}
else
{
var
aaChange
=
sChange
[
i
].
split
(
'
.
'
).
slice
(
-
1
)[
0
];
// LRRK2:NM_198578:exon1:c.T45C:p.T15T
var
variant
=
new
Variant
();
var
m
=
aaChange
.
match
(
/
([
a-zA-Z
]
+
)(\d
+
)([
a-zA-Z
])
+/
);
if
(
!
m
||
m
.
length
!=
4
)
continue
;
if
(
aaChange
.
endsWith
(
'
del
'
)
>
0
)
{
var
m
=
aaChange
.
match
(
/
(\d
+
)
_
(\d
+
)
/
);
[,
variant
.
posFrom
,
variant
.
posTo
]
=
m
;
variant
.
varType
=
'
Nonframeshift deletion
'
}
else
if
(
aaChange
.
indexOf
(
'
delins
'
)
>=
0
)
{
var
m
=
aaChange
.
match
(
/
([
A-Z
])(\d
+
)
delins
([
A-Z
]
+
)
/
);
[
,
variant
.
aaFrom
,
variant
.
posFrom
,
variant
.
aaTo
]
=
m
;
variant
.
aaTo
=
'
delins:
'
+
variant
.
aaTo
;
//This is because ProtVista can't handle insertions so we need to prefix it by 'd' which will place the variant into the 'd' line
variant
.
varType
=
'
Nonframeshift insertion
'
;
}
else
if
(
aaChange
.
endsWith
(
'
fs
'
))
{
var
m
=
aaChange
.
match
(
/
([
A-Z
])(\d
+
)
/
);
[
,
variant
.
aaFrom
,
variant
.
posFrom
]
=
m
;
if
(
change
.
indexOf
(
'
del
'
)
>=
0
)
variant
.
varType
=
'
Frameshift deletion
'
;
else
variant
.
varType
=
'
Frameshift insertion
'
;
}
else
{
[
,
variant
.
aaFrom
,
variant
.
posFrom
,
variant
.
aaTo
]
=
m
;
variant
.
varType
=
variant
.
aaFrom
==
variant
.
aaTo
?
'
Synonymous SNV
'
:
'
Nonsynonymous SNV
'
;
var
m
=
aaChange
.
match
(
/
([
a-zA-Z
]
+
)(\d
+
)([
a-zA-Z
])
+/
);
if
(
!
m
||
m
.
length
!=
4
)
continue
;
[
,
variant
.
aaFrom
,
variant
.
posFrom
,
variant
.
aaTo
]
=
m
;
variant
.
varType
=
variant
.
aaFrom
==
variant
.
aaTo
?
'
Synonymous SNV
'
:
'
Nonsynonymous SNV
'
;
}
vars
.
push
(
variant
);
}
catch
(
err
)
{
console
.
error
(
"
Problem with parsing variant
"
+
minervaVariant
.
getAminoAcidChange
(),
err
);
}
vars
.
push
(
variant
);
}
return
vars
;
...
...
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