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minerva
core
Commits
97411e82
Commit
97411e82
authored
Jun 10, 2021
by
Piotr Gawron
Browse files
data overlays are processed properly in zip file
parent
32647bee
Pipeline
#42997
failed with stage
in 25 minutes
Changes
36
Pipelines
1
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CHANGELOG
View file @
97411e82
minerva
(
16.0.0
~
beta
.1
)
stable
;
urgency
=
medium
*
Bug
fix
:
there
was
issue
with
updating
data
overlay
in
admin
panel
"Unknown
parameter: defaultOverlay"
*
Bug
fix
:
data
overlays
uploaded
in
complex
map
were
not
processed
properly
(#
1485
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Wed
,
9
Jun
2021
15
:
00
:
00
+
0200
...
...
service
/src/main/java/lcsb/mapviewer/
services/utils/data
/ColorSchemaColumn.java
→
converter
/src/main/java/lcsb/mapviewer/
converter
/ColorSchemaColumn.java
View file @
97411e82
package
lcsb.mapviewer.
services.utils.data
;
package
lcsb.mapviewer.
converter
;
import
java.util.HashSet
;
import
java.util.Set
;
...
...
service
/src/main/java/lcsb/mapviewer/
services/utils
/ColorSchemaReader.java
→
converter
/src/main/java/lcsb/mapviewer/
converter
/ColorSchemaReader.java
View file @
97411e82
package
lcsb.mapviewer.
services.utils
;
package
lcsb.mapviewer.
converter
;
import
java.awt.Color
;
import
java.io.*
;
import
java.lang.reflect.Field
;
import
java.util.*
;
import
org.apache.commons.lang3.StringUtils
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
lcsb.mapviewer.annotation.services.MiriamConnector
;
import
lcsb.mapviewer.common.*
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.common.exception.NotImplementedException
;
import
lcsb.mapviewer.common.geometry.ColorParser
;
import
lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping
;
import
lcsb.mapviewer.converter.zip.ZipEntryFileFactory
;
import
lcsb.mapviewer.model.map.*
;
import
lcsb.mapviewer.model.map.layout.ReferenceGenomeType
;
import
lcsb.mapviewer.model.map.species.*
;
import
lcsb.mapviewer.model.overlay.*
;
import
lcsb.mapviewer.services.utils.data.ColorSchemaColumn
;
/**
* Class that reads information about set of {@link DataOverlayEntry color
...
...
@@ -46,6 +43,22 @@ public class ColorSchemaReader {
*/
private
static
final
int
MIN_GV_RED_VALUE
=
128
;
private
static
Map
<
String
,
Class
<?
extends
BioEntity
>>
speciesMapping
;
static
{
speciesMapping
=
new
HashMap
<>();
speciesMapping
.
put
(
"protein"
,
Protein
.
class
);
speciesMapping
.
put
(
"gene"
,
Gene
.
class
);
speciesMapping
.
put
(
"complex"
,
Complex
.
class
);
speciesMapping
.
put
(
"simple_molecule"
,
SimpleMolecule
.
class
);
speciesMapping
.
put
(
"ion"
,
Ion
.
class
);
speciesMapping
.
put
(
"phenotype"
,
Phenotype
.
class
);
speciesMapping
.
put
(
"drug"
,
Drug
.
class
);
speciesMapping
.
put
(
"rna"
,
Rna
.
class
);
speciesMapping
.
put
(
"antisense_rna"
,
AntisenseRna
.
class
);
speciesMapping
.
put
(
"unknown"
,
Unknown
.
class
);
speciesMapping
.
put
(
"degraded"
,
Degraded
.
class
);
}
/**
* Object that parses colors from string.
*/
...
...
@@ -56,11 +69,6 @@ public class ColorSchemaReader {
*/
private
Logger
logger
=
LogManager
.
getLogger
();
/**
* Objects that manipulates {@link MiriamData}.
*/
private
MiriamConnector
mc
=
new
MiriamConnector
();
/**
* Reads information about set of {@link DataOverlayEntry color schemas} from
* the input stream.
...
...
@@ -196,9 +204,9 @@ public class ColorSchemaReader {
if
(
typeColumn
!=
null
)
{
String
[]
types
=
values
[
typeColumn
].
split
(
","
);
for
(
String
string
:
types
)
{
SpeciesMapping
mapping
=
S
peciesMapping
.
get
MappingByString
(
string
);
if
(
mapping
!=
null
)
{
schema
.
addType
(
mapping
.
getModelC
lazz
()
);
Class
<?
extends
BioEntity
>
clazz
=
s
peciesMapping
.
get
(
string
.
toLowerCase
()
);
if
(
clazz
!=
null
)
{
schema
.
addType
(
c
lazz
);
}
else
{
throw
new
InvalidDataOverlayException
(
"[Line "
+
lineIndex
+
"] Unknown class type: "
+
string
+
"."
);
}
...
...
@@ -274,10 +282,10 @@ public class ColorSchemaReader {
private
void
processGeneralIdentifier
(
String
string
,
DataOverlayEntry
schema
,
String
errorPrefix
)
throws
InvalidDataOverlayException
{
if
(
mc
.
isValidIdentifier
(
string
))
{
try
{
schema
.
addMiriamData
(
MiriamType
.
getMiriamDataFromIdentifier
(
string
));
}
else
{
throw
new
InvalidDataOverlayException
(
errorPrefix
+
" Invalid identifier: "
+
string
);
}
catch
(
InvalidArgumentException
e
)
{
throw
new
InvalidDataOverlayException
(
errorPrefix
+
" Invalid identifier: "
+
string
,
e
);
}
}
...
...
@@ -564,16 +572,13 @@ public class ColorSchemaReader {
String
[]
types
=
typesString
.
split
(
","
);
for
(
String
string
:
types
)
{
if
(!
string
.
isEmpty
())
{
SpeciesMapping
mapping
=
S
peciesMapping
.
get
MappingByString
(
string
);
if
(
mapping
!=
null
)
{
result
.
add
(
mapping
.
getModelC
lazz
()
);
Class
<?
extends
BioEntity
>
clazz
=
s
peciesMapping
.
get
(
string
.
toLowerCase
()
);
if
(
clazz
!=
null
)
{
result
.
add
(
c
lazz
);
}
else
{
String
validStrings
=
""
;
for
(
SpeciesMapping
speciesMapping
:
SpeciesMapping
.
values
())
{
validStrings
+=
speciesMapping
.
getCellDesignerString
()
+
", "
;
}
throw
new
InvalidDataOverlayException
(
errorPrefix
+
"Unknown class type: "
+
string
+
". Valid values are: "
+
validStrings
);
errorPrefix
+
"Unknown class type: "
+
string
+
". Valid values are: "
+
StringUtils
.
join
(
speciesMapping
.
values
(),
","
));
}
}
}
...
...
converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
View file @
97411e82
...
...
@@ -21,8 +21,7 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
import
lcsb.mapviewer.model.map.model.*
;
import
lcsb.mapviewer.model.map.reaction.Reaction
;
import
lcsb.mapviewer.model.map.species.*
;
import
lcsb.mapviewer.model.overlay.DataOverlayType
;
import
lcsb.mapviewer.model.overlay.DataOverlay
;
import
lcsb.mapviewer.model.overlay.*
;
/**
* This class allows to create complex {@link Model} that contains submaps. It's
...
...
@@ -304,9 +303,10 @@ public class ComplexZipConverter {
* @return {@link DataOverlay} for a given {@link LayoutZipEntryFile}
* @throws IOException
* thrown when there is a problem with accessing {@link ZipFile}
* @throws InvalidInputDataExecption
*/
public
DataOverlay
layoutZipEntryFileToLayout
(
ComplexZipConverterParams
params
,
ZipFile
zipFile
,
ZipEntry
entry
,
LayoutZipEntryFile
layoutEntry
,
int
order
)
throws
IOException
{
LayoutZipEntryFile
layoutEntry
,
int
order
)
throws
IOException
,
InvalidInputDataExecption
{
DataOverlay
layout
=
new
DataOverlay
();
layout
.
setDescription
(
layoutEntry
.
getDescription
());
UploadedFileEntry
fileEntry
=
new
UploadedFileEntry
();
...
...
@@ -329,6 +329,14 @@ public class ComplexZipConverter {
layout
.
setPublic
(
true
);
layout
.
setName
(
layoutEntry
.
getName
());
layout
.
setOrderIndex
(
order
);
ColorSchemaReader
reader
=
new
ColorSchemaReader
();
ByteArrayInputStream
baos
=
new
ByteArrayInputStream
(
fileEntry
.
getFileContent
());
try
{
layout
.
addEntries
(
reader
.
readColorSchema
(
baos
,
parameters
));
}
catch
(
InvalidDataOverlayException
e
)
{
throw
new
InvalidInputDataExecption
(
e
);
}
return
layout
;
}
...
...
converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
View file @
97411e82
...
...
@@ -7,7 +7,9 @@ import org.junit.runners.Suite.SuiteClasses;
import
lcsb.mapviewer.converter.annotation.XmlAnnotationParserTest
;
@RunWith
(
Suite
.
class
)
@SuiteClasses
({
ComplexZipConverterParamsTest
.
class
,
@SuiteClasses
({
ColorSchemaReaderTest
.
class
,
ComplexZipConverterParamsTest
.
class
,
ComplexZipConverterTest
.
class
,
OverviewParserTest
.
class
,
ProjectFactoryTest
.
class
,
...
...
service
/src/test/java/lcsb/mapviewer/
services/utils
/ColorSchemaReaderTest.java
→
converter
/src/test/java/lcsb/mapviewer/
converter
/ColorSchemaReaderTest.java
View file @
97411e82
package
lcsb.mapviewer.
services.utils
;
package
lcsb.mapviewer.
converter
;
import
static
org
.
junit
.
Assert
.*;
...
...
@@ -12,16 +12,13 @@ import org.apache.logging.log4j.LogManager;
import
org.apache.logging.log4j.Logger
;
import
org.junit.*
;
import
lcsb.mapviewer.commands.ColorExtractor
;
import
lcsb.mapviewer.commands.ColorModelCommand
;
import
lcsb.mapviewer.common.Configuration
;
import
lcsb.mapviewer.common.TextFileUtils
;
import
lcsb.mapviewer.model.map.BioEntity
;
import
lcsb.mapviewer.model.map.MiriamData
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.overlay.*
;
import
lcsb.mapviewer.services.ServiceTestFunctions
;
public
class
ColorSchemaReaderTest
extends
Service
TestFunctions
{
public
class
ColorSchemaReaderTest
extends
Converter
TestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
ColorSchemaReader
reader
;
...
...
@@ -37,17 +34,17 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public
void
testReadSchema
()
throws
Exception
{
Collection
<
DataOverlayEntry
>
schemas
=
reader
.
readColorSchema
(
"testFiles/
enricoData
/ageing.txt"
);
Collection
<
DataOverlayEntry
>
schemas
=
reader
.
readColorSchema
(
"testFiles/
coloring
/ageing.txt"
);
assertNotNull
(
schemas
);
assertEquals
(
412
,
schemas
.
size
());
schemas
=
reader
.
readColorSchema
(
"testFiles/
enricoData
/ge001.txt"
);
schemas
=
reader
.
readColorSchema
(
"testFiles/
coloring
/ge001.txt"
);
assertNotNull
(
schemas
);
assertEquals
(
3057
,
schemas
.
size
());
schemas
=
reader
.
readColorSchema
(
"testFiles/
enricoData
/ge005.txt"
);
schemas
=
reader
.
readColorSchema
(
"testFiles/
coloring
/ge005.txt"
);
assertNotNull
(
schemas
);
assertEquals
(
4338
,
schemas
.
size
());
...
...
@@ -174,7 +171,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
assertEquals
(
1
,
collection
.
size
());
DataOverlayEntry
schema
=
collection
.
iterator
().
next
();
assertEquals
(
"re1"
,
schema
.
getElementId
());
assertEquals
(
3.0
,
schema
.
getLineWidth
(),
EPSILON
);
assertEquals
(
3.0
,
schema
.
getLineWidth
(),
Configuration
.
EPSILON
);
assertEquals
(
Color
.
RED
,
schema
.
getColor
());
}
...
...
@@ -186,19 +183,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
assertEquals
(
3
,
schemas
.
size
());
}
@Test
public
void
testColoring3
()
throws
Exception
{
ColorExtractor
colorExtractor
=
new
ColorExtractor
(
Color
.
RED
,
Color
.
GREEN
,
Color
.
BLUE
,
Color
.
WHITE
);
Model
model
=
getModelForFile
(
"testFiles/coloring/protein_to_color.xml"
,
false
);
Collection
<
DataOverlayEntry
>
schemas
=
reader
.
readColorSchema
(
"testFiles/coloring/problematicSchema.txt"
);
ColorModelCommand
factory
=
new
ColorModelCommand
(
model
,
schemas
,
colorExtractor
);
factory
.
execute
();
assertFalse
(
model
.
getElementByElementId
(
"sa1"
).
getFillColor
().
equals
(
Color
.
WHITE
));
}
@Test
public
void
testColoringWithValueOrColor
()
throws
Exception
{
Map
<
String
,
String
>
params
=
new
HashMap
<>();
...
...
converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
View file @
97411e82
...
...
@@ -284,17 +284,18 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
public
void
testLayoutZipEntryFileToLayoutOrder
()
throws
Exception
{
ComplexZipConverter
converter
=
new
ComplexZipConverter
(
MockConverter
.
class
);
ComplexZipConverterParams
params
=
new
ComplexZipConverterParams
();
ZipFile
file
=
Mockito
.
mock
(
ZipFile
.
class
);
params
.
zipFile
(
file
);
ZipFile
file
1
=
Mockito
.
mock
(
ZipFile
.
class
);
ZipFile
file2
=
Mockito
.
mock
(
ZipFile
.
class
);
LayoutZipEntryFile
entry1
=
new
LayoutZipEntryFile
(
"overlay1.txt"
,
"name"
,
"desc1"
);
LayoutZipEntryFile
entry2
=
new
LayoutZipEntryFile
(
"overlay2.txt"
,
"name"
,
"desc1"
);
params
.
entry
(
entry1
);
params
.
entry
(
entry2
);
ZipEntry
entry
=
Mockito
.
mock
(
ZipEntry
.
class
);
Mockito
.
when
(
file
.
getInputStream
(
entry
)).
thenReturn
(
new
ByteArrayInputStream
(
""
.
getBytes
()));
Mockito
.
when
(
file1
.
getInputStream
(
entry
)).
thenReturn
(
new
ByteArrayInputStream
(
"name\tvalue\n"
.
getBytes
()));
Mockito
.
when
(
file2
.
getInputStream
(
entry
)).
thenReturn
(
new
ByteArrayInputStream
(
"name\tvalue\n"
.
getBytes
()));
DataOverlay
overlay1
=
converter
.
layoutZipEntryFileToLayout
(
params
,
file
,
entry
,
entry1
,
1
);
DataOverlay
overlay2
=
converter
.
layoutZipEntryFileToLayout
(
params
,
file
,
entry
,
entry2
,
2
);
DataOverlay
overlay1
=
converter
.
layoutZipEntryFileToLayout
(
params
,
file
1
,
entry
,
entry1
,
1
);
DataOverlay
overlay2
=
converter
.
layoutZipEntryFileToLayout
(
params
,
file
2
,
entry
,
entry2
,
2
);
assertTrue
(
overlay1
.
getOrderIndex
()
>
0
);
assertTrue
(
overlay2
.
getOrderIndex
()
>
overlay1
.
getOrderIndex
());
}
...
...
converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
View file @
97411e82
...
...
@@ -18,8 +18,10 @@ import lcsb.mapviewer.model.Project;
import
lcsb.mapviewer.model.map.*
;
import
lcsb.mapviewer.model.map.layout.graphics.Layer
;
import
lcsb.mapviewer.model.map.layout.graphics.LayerText
;
import
lcsb.mapviewer.model.map.model.*
;
import
lcsb.mapviewer.model.map.model.Model
;
import
lcsb.mapviewer.model.map.model.ModelFullIndexed
;
import
lcsb.mapviewer.model.map.species.GenericProtein
;
import
lcsb.mapviewer.model.overlay.DataOverlay
;
public
class
ProjectFactoryTest
extends
ConverterTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
...
...
@@ -221,4 +223,28 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
return
result
;
}
@Test
public
void
testWithOverlay
()
throws
Exception
{
ComplexZipConverter
converter
=
new
ComplexZipConverter
(
MockConverter
.
class
);
ProjectFactory
projectFactory
=
new
ProjectFactory
(
converter
);
ZipFile
zipFile
=
new
ZipFile
(
"testFiles/complex_model_with_layouts.zip"
);
ComplexZipConverterParams
params
=
new
ComplexZipConverterParams
();
params
.
zipFile
(
zipFile
);
ZipEntryFileFactory
factory
=
new
ZipEntryFileFactory
();
Enumeration
<?
extends
ZipEntry
>
entries
=
zipFile
.
entries
();
while
(
entries
.
hasMoreElements
())
{
ZipEntry
entry
=
entries
.
nextElement
();
if
(!
entry
.
isDirectory
())
{
params
.
entry
(
factory
.
createZipEntryFile
(
entry
,
zipFile
));
}
}
Project
project
=
projectFactory
.
create
(
params
);
assertNotNull
(
project
);
assertEquals
(
1
,
project
.
getDataOverlays
().
size
());
DataOverlay
overlay
=
project
.
getDataOverlays
().
get
(
0
);
assertTrue
(
overlay
.
getEntries
().
size
()
>
0
);
}
}
service
/testFiles/
enricoData
/ageing.txt
→
converter
/testFiles/
coloring
/ageing.txt
View file @
97411e82
File moved
service
/testFiles/
enricoData
/ge001.txt
→
converter
/testFiles/
coloring
/ge001.txt
View file @
97411e82
File moved
service
/testFiles/
enricoData
/ge005.txt
→
converter
/testFiles/
coloring
/ge005.txt
View file @
97411e82
File moved
converter/testFiles/coloring/gene_variants.txt
0 → 100644
View file @
97411e82
#TYPE=GENETIC_VARIANT
#GENOME_TYPE=UCSC
#GENOME_VERSION=hg38
position original_dna alternative_dna gene_name description color contig
10146 AC A DDX11L1 upstream #ff0000 chr1
10439 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1
10583 G A DDX11L1;WASH7P upstream;downstream #ff0002 chr1
10611 C G DDX11L1;WASH7P upstream;downstream #ff0003 chr1
10616 CCGCCGTTGCAAAGGCGCGCCG C DDX11L1;WASH7P upstream;downstream #ff0004 chr1
10904 G A DDX11L1;WASH7P upstream;downstream #ff0005 chr1
12783 G A DDX11L1 intronic #ff0006 chr1
13116 T G DDX11L1 intronic #ff0007 chr1
13118 A G DDX11L1 intronic #ff0008 chr1
13143 G C DDX11L1 intronic #ff0009 chr1
13273 G C DDX11L1 intronic #ff0010 chr1
13302 C T DDX11L1 intronic #ff0011 chr1
13417 C CGAGA DDX11L1 exonic #ff0012 chr1
13550 G A DDX11L1 exonic #ff0013 chr1
13656 CAG C DDX11L1 UTR3 #ff0014 chr1
13668 G A DDX11L1 UTR3 #ff0015 chr1
13813 T G DDX11L1 UTR3 #ff0016 chr1
13838 C T DDX11L1 UTR3 #ff0017 chr1
13868 A G DDX11L1 UTR3 #ff0018 chr1
13896 C A DDX11L1 UTR3 #ff0019 chr1
13957 TC T DDX11L1 UTR3 #ff0020 chr1
14354 C A DDX11L1 UTR3 #ff0021 chr1
14464 A T WASH7P ncRNA_exonic #ff0022 chr1
14653 C T WASH7P ncRNA_exonic #ff0023 chr1
14671 G C WASH7P ncRNA_exonic #ff0024 chr1
14673 G C WASH7P ncRNA_exonic #ff0025 chr1
14677 G A WASH7P ncRNA_exonic #ff0026 chr1
14699 C G WASH7P ncRNA_exonic #ff0027 chr1
14907 A G WASH7P ncRNA_exonic #ff0028 chr1
14930 A G WASH7P ncRNA_exonic #ff0029 chr1
14933 G A WASH7P ncRNA_exonic #ff0030 chr1
14976 G A WASH7P ncRNA_exonic #ff0031 chr1
15118 A G WASH7P ncRNA_exonic #ff0032 chr1
15190 G A WASH7P ncRNA_exonic #ff0033 chr1
15211 T G WASH7P ncRNA_exonic #ff0034 chr1
15274 A G,T WASH7P ncRNA_exonic #ff0035 chr1
15447 A G WASH7P ncRNA_exonic #ff0036 chr1
15688 C T WASH7P ncRNA_exonic #ff0037 chr1
15820 G T WASH7P ncRNA_exonic #ff0038 chr1
15903 G GC WASH7P ncRNA_exonic #ff0039 chr1
16014 C T WASH7P ncRNA_exonic #ff0040 chr1
16068 T C WASH7P ncRNA_exonic #ff0041 chr1
16103 T G WASH7P ncRNA_exonic #ff0042 chr1
16206 T A WASH7P ncRNA_exonic #ff0043 chr1
16226 AG A WASH7P ncRNA_exonic #ff0044 chr1
16257 G C WASH7P ncRNA_exonic #ff0045 chr1
16288 C G WASH7P ncRNA_exonic #ff0046 chr1
16298 C T WASH7P ncRNA_exonic #ff0047 chr1
16378 T C WASH7P ncRNA_exonic #ff0048 chr1
16487 T C WASH7P ncRNA_exonic #ff0049 chr1
16495 G C WASH7P ncRNA_exonic #ff0050 chr1
16497 A G WASH7P ncRNA_exonic #ff0051 chr1
16534 C T WASH7P ncRNA_exonic #ff0052 chr1
16571 G A WASH7P ncRNA_exonic #ff0053 chr1
16682 G A WASH7P ncRNA_exonic #ff0054 chr1
16688 G A WASH7P ncRNA_exonic #ff0055 chr1
16719 T A WASH7P ncRNA_exonic #ff0056 chr1
16737 G T WASH7P ncRNA_exonic #ff0057 chr1
16742 G C WASH7P ncRNA_exonic #ff0058 chr1
16809 C G WASH7P ncRNA_intronic #ff0059 chr1
16841 G T WASH7P ncRNA_intronic #ff0060 chr1
16949 A C WASH7P ncRNA_exonic #ff0061 chr1
16963 G A WASH7P ncRNA_exonic #ff0062 chr1
16977 G A WASH7P ncRNA_exonic #ff0063 chr1
17020 G A WASH7P ncRNA_exonic #ff0064 chr1
17222 A G WASH7P ncRNA_intronic #ff0065 chr1
17385 G A MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 ncRNA_exonic #ff0066 chr1
17408 C G MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 ncRNA_exonic #ff0067 chr1
17538 C A WASH7P ncRNA_exonic #ff0068 chr1
17594 C T WASH7P ncRNA_exonic #ff0069 chr1
17614 G A WASH7P ncRNA_exonic #ff0070 chr1
17697 G C WASH7P ncRNA_exonic #ff0071 chr1
17730 C A WASH7P ncRNA_exonic #ff0072 chr1
17746 A G WASH7P ncRNA_exonic;splicing #ff0073 chr1
17765 G A WASH7P ncRNA_exonic #ff0074 chr1
17961 TG T WASH7P ncRNA_exonic #ff0075 chr1
19004 A G WASH7P ncRNA_exonic #ff0076 chr1
19322 C T WASH7P ncRNA_exonic #ff0077 chr1
19583 A G WASH7P ncRNA_exonic #ff0078 chr1
19592 T C WASH7P ncRNA_exonic #ff0079 chr1
19600 A T WASH7P ncRNA_exonic #ff0080 chr1
19604 T C WASH7P ncRNA_exonic #ff0081 chr1
19776 A G WASH7P ncRNA_intronic #ff0082 chr1
19788 C T WASH7P ncRNA_intronic #ff0083 chr1
19858 C T WASH7P ncRNA_intronic #ff0084 chr1
19942 G C WASH7P ncRNA_intronic #ff0085 chr1
20094 TAA T WASH7P ncRNA_intronic #ff0086 chr1
20098 CAG C WASH7P ncRNA_intronic #ff0087 chr1
20129 C T WASH7P ncRNA_intronic #ff0088 chr1
20136 T C WASH7P ncRNA_intronic #ff0089 chr1
20144 G A WASH7P ncRNA_intronic #ff0090 chr1
20191 T G WASH7P ncRNA_intronic #ff0091 chr1
20206 C T WASH7P ncRNA_intronic #ff0092 chr1
20207 G A WASH7P ncRNA_intronic #ff0093 chr1
20212 A G WASH7P ncRNA_intronic #ff0094 chr1
20227 T A WASH7P ncRNA_intronic #ff0095 chr1
20235 G A WASH7P ncRNA_intronic #ff0096 chr1
20245 G A WASH7P ncRNA_intronic #ff0097 chr1
20250 T C WASH7P ncRNA_intronic #ff0098 chr1
converter/testFiles/coloring/gene_variants_aa_change.txt
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#TYPE=GENETIC_VARIANT
#GENOME_TYPE=UCSC
#GENOME_VERSION=hg38
position original_dna alternative_dna gene_name description color contig allele_frequency variant_identifier amino_acid_change
10146 AC A DDX11L1 upstream #ff0000 chr1 0.8 identifier_1 LRRK2:NM_198578:exon1:c.T45C:p.T15T
10439 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.5 identifier_2 LRRK2:NM_198578:exon1:c.C67T:p.L23L
10441 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.2 identifier_3 frameshift_insertion
10443 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.9 identifier_4
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/testFiles/coloring/gene_variants_all_freq.txt
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/testFiles/coloring/gene_variants_all_freq.txt
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