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Mirrors
biopet.biopet
Commits
2fdf69e7
Commit
2fdf69e7
authored
Sep 21, 2015
by
Peter van 't Hof
Browse files
This will remove tempfiles on exit
parent
6300d051
Changes
18
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
2fdf69e7
...
...
@@ -231,6 +231,7 @@ object ReportBuilder {
case
Some
(
template
)
=>
template
case
_
=>
val
tempFile
=
File
.
createTempFile
(
"ssp-template"
,
new
File
(
location
).
getName
)
tempFile
.
deleteOnExit
()
IoUtils
.
copyStreamToFile
(
getClass
.
getResourceAsStream
(
location
),
tempFile
)
templateCache
+=
location
->
tempFile
tempFile
...
...
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
2fdf69e7
...
...
@@ -625,6 +625,7 @@ object VcfStats extends ToolCommand {
def
executeRscript
(
resource
:
String
,
args
:
Array
[
String
])
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
resource
)
val
file
=
File
.
createTempFile
(
"script."
,
"."
+
resource
)
file
.
deleteOnExit
()
val
os
=
new
FileOutputStream
(
file
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
View file @
2fdf69e7
...
...
@@ -31,6 +31,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test
def
testMainVcf
=
{
val
tmp
=
File
.
createTempFile
(
"basty_out"
,
".fa"
)
tmp
.
deleteOnExit
()
val
tmppath
=
tmp
.
getAbsolutePath
tmp
.
deleteOnExit
()
...
...
@@ -40,6 +41,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test
def
testMainVcfAndBam
=
{
val
tmp
=
File
.
createTempFile
(
"basty_out"
,
".fa"
)
tmp
.
deleteOnExit
()
val
tmppath
=
tmp
.
getAbsolutePath
tmp
.
deleteOnExit
()
...
...
@@ -49,6 +51,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
@Test
def
testMainVcfAndBamMore
=
{
val
tmp
=
File
.
createTempFile
(
"basty_out"
,
".fa"
)
tmp
.
deleteOnExit
()
val
tmppath
=
tmp
.
getAbsolutePath
tmp
.
deleteOnExit
()
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
View file @
2fdf69e7
...
...
@@ -56,6 +56,7 @@ class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
def
testMain
()
=
{
//TODO: Test output file
val
output
=
File
.
createTempFile
(
"testMain"
,
".biopetflagstat"
)
output
.
deleteOnExit
()
main
(
Array
(
"-I"
,
bam
.
getAbsolutePath
,
"-o"
,
output
.
toString
))
}
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
View file @
2fdf69e7
...
...
@@ -23,7 +23,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testMain
()
=
{
val
temp
=
File
.
createTempFile
(
"out"
,
".fastq"
)
temp
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
fq
,
"-o"
,
temp
.
getAbsolutePath
)
main
(
args
)
}
...
...
@@ -31,6 +31,7 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testManyOutMain
()
=
{
val
files
=
(
0
until
10
).
map
(
_
=>
File
.
createTempFile
(
"out"
,
".fastq"
))
files
.
foreach
(
_
.
deleteOnExit
())
var
args
=
Array
(
"-I"
,
fq
)
files
.
foreach
(
x
=>
args
++=
Array
(
"-o"
,
x
.
getAbsolutePath
))
main
(
args
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
View file @
2fdf69e7
...
...
@@ -29,6 +29,7 @@ class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers
def
testMain
()
=
{
val
outputFile
=
File
.
createTempFile
(
"repeats"
,
".tsv"
)
outputFile
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
bam
,
"-b"
,
bed
,
"-o"
,
outputFile
.
toString
)
main
(
args
)
}
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
View file @
2fdf69e7
...
...
@@ -28,6 +28,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testMain
()
=
{
val
tmp
=
File
.
createTempFile
(
"mpileup"
,
".vcf"
)
tmp
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
pileup
,
"--sample"
,
"test"
,
"-o"
,
tmp
.
getAbsolutePath
)
main
(
args
)
...
...
@@ -36,6 +37,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
validateOutVcf
()
=
{
val
tmp
=
File
.
createTempFile
(
"mpileup"
,
".vcf"
)
tmp
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
pileup
,
"--sample"
,
"test"
,
"-o"
,
tmp
.
getAbsolutePath
,
"--minDP"
,
"1"
,
"--minAP"
,
"1"
)
main
(
args
)
...
...
@@ -51,6 +53,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
extraValidateOutVcf
()
=
{
val
tmp
=
File
.
createTempFile
(
"mpileup"
,
".vcf"
)
tmp
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
pileup
,
"--sample"
,
"test"
,
"-o"
,
tmp
.
getAbsolutePath
,
"--minDP"
,
"1"
,
"--minAP"
,
"1"
)
main
(
args
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
View file @
2fdf69e7
...
...
@@ -26,6 +26,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testMain
()
=
{
val
temp
=
File
.
createTempFile
(
"out"
,
".fastq"
)
temp
.
deleteOnExit
()
val
args
=
Array
(
"-i"
,
fq
,
"-o"
,
temp
.
getAbsolutePath
,
"-s"
,
"AAA"
)
main
(
args
)
...
...
@@ -34,6 +35,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testOutput
()
=
{
val
temp
=
File
.
createTempFile
(
"out"
,
".fastq"
)
temp
.
deleteOnExit
()
val
args
=
Array
(
"-i"
,
fq
,
"-o"
,
temp
.
getAbsolutePath
,
"-s"
,
"AAA"
)
main
(
args
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
View file @
2fdf69e7
...
...
@@ -22,6 +22,7 @@ class SageCountFastqTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def
testMain
()
=
{
val
temp
=
File
.
createTempFile
(
"out"
,
".fastq"
)
temp
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
fq
,
"-o"
,
temp
.
getAbsolutePath
)
main
(
args
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
View file @
2fdf69e7
...
...
@@ -29,9 +29,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
val
input
=
resourcePath
(
"/mini.transcriptome.fa"
)
val
output
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
output
.
deleteOnExit
()
val
noTagsOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
noTagsOutput
.
deleteOnExit
()
val
antiTagsOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
antiTagsOutput
.
deleteOnExit
()
val
allGenesOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
allGenesOutput
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
input
,
"-o"
,
output
.
getAbsolutePath
,
"--tag"
,
"CATG"
,
"--length"
,
"17"
,
"--noTagsOutput"
,
noTagsOutput
.
getAbsolutePath
,
"--noAntiTagsOutput"
,
...
...
@@ -52,9 +56,13 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
def
testOutPut
=
{
val
input
=
resourcePath
(
"/mini.transcriptome.fa"
)
val
output
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
output
.
deleteOnExit
()
val
noTagsOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
noTagsOutput
.
deleteOnExit
()
val
antiTagsOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
antiTagsOutput
.
deleteOnExit
()
val
allGenesOutput
=
File
.
createTempFile
(
"sageCreateLibrary"
,
".tsv"
)
allGenesOutput
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
input
,
"-o"
,
output
.
getAbsolutePath
,
"--tag"
,
"CATG"
,
"--length"
,
"17"
,
"--noTagsOutput"
,
noTagsOutput
.
getAbsolutePath
,
"--noAntiTagsOutput"
,
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
View file @
2fdf69e7
...
...
@@ -26,9 +26,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val
tagLib
=
resourcePath
(
"/sageTest.tsv"
)
val
sense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
sense
.
deleteOnExit
()
val
allSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
allSense
.
deleteOnExit
()
val
antiSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
antiSense
.
deleteOnExit
()
val
allAntiSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
allAntiSense
.
deleteOnExit
()
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
input
,
"--tagLib"
,
tagLib
,
"--countSense"
,
sense
.
getAbsolutePath
,
"--countAllSense"
,
allSense
.
getAbsolutePath
,
...
...
@@ -50,9 +54,13 @@ class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matcher
val
tagLib
=
resourcePath
(
"/sageTest.tsv"
)
val
sense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
sense
.
deleteOnExit
()
val
allSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
allSense
.
deleteOnExit
()
val
antiSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
antiSense
.
deleteOnExit
()
val
allAntiSense
=
File
.
createTempFile
(
"SageCreateTagCountsTEst"
,
".tsv"
)
allAntiSense
.
deleteOnExit
()
main
(
Array
(
"-I"
,
input
,
"--tagLib"
,
tagLib
,
"--countSense"
,
sense
.
getAbsolutePath
,
"--countAllSense"
,
allSense
.
getAbsolutePath
,
"--countAntiSense"
,
antiSense
.
getAbsolutePath
,
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
View file @
2fdf69e7
...
...
@@ -21,6 +21,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def
testCorrectSampleTsv
=
{
val
tsv
=
resourcePath
(
"/sample.tsv"
)
val
output
=
File
.
createTempFile
(
"testCorrectSampleTsv"
,
".json"
)
output
.
deleteOnExit
()
noException
should
be
thrownBy
main
(
Array
(
"-i"
,
tsv
,
"-o"
,
output
.
toString
))
}
...
...
@@ -29,6 +30,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def
testNoSampleColumn
()
=
{
val
tsv
=
resourcePath
(
"/no_sample.tsv"
)
val
output
=
File
.
createTempFile
(
"testNoSampleColumn"
,
".json"
)
output
.
deleteOnExit
()
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
,
"-o"
,
output
.
toString
))
thrown
.
getMessage
should
equal
(
"Sample column does not exist in: "
+
tsv
)
}
...
...
@@ -37,6 +39,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def
testNumberInLibs
=
{
val
tsv
=
resourcePath
(
"/number.tsv"
)
val
output
=
File
.
createTempFile
(
"testNumberInLibs"
,
".json"
)
output
.
deleteOnExit
()
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
,
"-o"
,
output
.
toString
))
thrown
.
getMessage
should
equal
(
"Sample or library may not start with a number"
)
}
...
...
@@ -45,6 +48,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
def
testSampleIDs
=
{
val
tsv
=
resourcePath
(
"/same.tsv"
)
val
output
=
File
.
createTempFile
(
"testSampleIDs"
,
".json"
)
output
.
deleteOnExit
()
val
thrown
=
the
[
IllegalStateException
]
thrownBy
main
(
Array
(
"-i"
,
tsv
,
"-o"
,
output
.
toString
))
thrown
.
getMessage
should
equal
(
"Combination of Sample_ID_1 and Lib_ID_1 is found multiple times"
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
View file @
2fdf69e7
...
...
@@ -24,6 +24,7 @@ class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
def
testMain
=
{
val
tsv
=
resourcePath
(
"/test.summary.json"
)
val
output
=
File
.
createTempFile
(
"main"
,
"tsv"
)
output
.
deleteOnExit
()
noException
should
be
thrownBy
main
(
Array
(
"-s"
,
tsv
,
"-p"
,
"something=flexiprep:settings:skip_trim"
,
"-m"
,
"root"
,
"-o"
,
output
.
toString
))
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
View file @
2fdf69e7
...
...
@@ -47,50 +47,57 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
val
rand
=
new
Random
()
@Test
def
testOutputTypeVcf
()
=
{
val
tmpPath
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
).
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ"
)
val
tmpFile
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ"
)
main
(
arguments
)
}
@Test
def
testOutputTypeVcfGz
()
=
{
val
tmpPath
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf.gz"
).
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ"
)
val
tmpFile
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf.gz"
)
tmpFile
.
deleteOnExit
()
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ"
)
main
(
arguments
)
}
@Test
def
testOutputTypeBcf
()
=
{
val
tmpPath
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".bcf"
).
getAbsolutePath
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ"
)
val
tmpFile
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".bcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ"
)
main
(
arguments
)
}
@Test
def
testOutputFieldException
=
{
val
tmpPath
=
File
.
createTempFile
(
"VCFWithVCf"
,
".vcf"
).
getAbsolutePath
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ:AC"
)
val
tmpFile
=
File
.
createTempFile
(
"VCFWithVCf"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ:AC"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
args
)
val
thrown
=
the
[
IllegalArgumentException
]
thrownBy
main
(
args
)
thrown
.
getMessage
should
equal
(
"Field 'AC' already exists in input vcf"
)
}
@Test
def
testInputFieldException
=
{
val
tmpPath
=
File
.
createTempFile
(
"VCFWithVCf"
,
".vcf"
).
getAbsolutePath
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
unveppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ:NEW_CSQ"
)
val
tmpFile
=
File
.
createTempFile
(
"VCFWithVCf"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
unveppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ:NEW_CSQ"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
args
)
val
thrown
=
the
[
IllegalArgumentException
]
thrownBy
main
(
args
)
thrown
.
getMessage
should
equal
(
"Field 'CSQ' does not exist in secondary vcf"
)
}
@Test
def
testMinMethodException
=
{
val
tmpPath
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
).
getAbsolutePath
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ:CSQ:min"
)
val
tmpFile
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ:CSQ:min"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
args
)
val
thrown
=
the
[
IllegalArgumentException
]
thrownBy
main
(
args
)
thrown
.
getMessage
should
equal
(
"Type of field CSQ is not numeric"
)
}
@Test
def
testMaxMethodException
=
{
val
tmpPath
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
).
getAbsolutePath
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpPath
,
"-f"
,
"CSQ:CSQ:max"
)
val
tmpFile
=
File
.
createTempFile
(
"VcfWithVcf_"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
args
=
Array
(
"-I"
,
unveppedPath
,
"-s"
,
veppedPath
,
"-o"
,
tmpFile
.
getAbsolutePath
,
"-f"
,
"CSQ:CSQ:max"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
args
)
val
thrown
=
the
[
IllegalArgumentException
]
thrownBy
main
(
args
)
thrown
.
getMessage
should
equal
(
"Type of field CSQ is not numeric"
)
...
...
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
View file @
2fdf69e7
...
...
@@ -47,38 +47,44 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val
rand
=
new
Random
()
@Test
def
testGzOutputExplode
()
:
Unit
=
{
val
tmpPath
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf.gz"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpPath
,
"-m"
,
"explode"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf.gz"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"explode"
)
main
(
arguments
)
}
@Test
def
testVcfOutputExplode
()
:
Unit
=
{
val
tmpPath
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpPath
,
"-m"
,
"explode"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"explode"
)
main
(
arguments
)
}
@Test
def
testBcfOutputExplode
()
:
Unit
=
{
val
tmp_path
=
File
.
createTempFile
(
"VepNormalizer_"
,
".bcf"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmp_path
,
"-m"
,
"explode"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".bcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"explode"
)
main
(
arguments
)
}
@Test
def
testGzOutputStandard
()
:
Unit
=
{
val
tmp_path
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf.gz"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmp_path
,
"-m"
,
"standard"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf.gz"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"standard"
)
main
(
arguments
)
}
@Test
def
testVcfOutputStandard
()
:
Unit
=
{
val
tmp_path
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmp_path
,
"-m"
,
"standard"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".vcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"standard"
)
main
(
arguments
)
}
@Test
def
testBcfOutputStandard
()
:
Unit
=
{
val
tmp_path
=
File
.
createTempFile
(
"VepNormalizer_"
,
".bcf"
).
getAbsolutePath
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmp_path
,
"-m"
,
"standard"
)
val
tmpFile
=
File
.
createTempFile
(
"VepNormalizer_"
,
".bcf"
)
tmpFile
.
deleteOnExit
()
val
arguments
:
Array
[
String
]
=
Array
(
"-I"
,
vepped_path
,
"-O"
,
tmpFile
.
getAbsolutePath
,
"-m"
,
"standard"
)
main
(
arguments
)
}
...
...
public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
View file @
2fdf69e7
...
...
@@ -28,7 +28,11 @@ trait Rscript extends Configurable {
}
else
{
val
rScript
:
File
=
dir
match
{
case
Some
(
dir
)
=>
new
File
(
dir
,
script
.
getName
)
case
_
=>
File
.
createTempFile
(
script
.
getName
,
".R"
)
case
_
=>
{
val
file
=
File
.
createTempFile
(
script
.
getName
,
".R"
)
file
.
deleteOnExit
()
file
}
}
if
(!
rScript
.
getParentFile
.
exists
)
rScript
.
getParentFile
.
mkdirs
...
...
public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
View file @
2fdf69e7
...
...
@@ -228,6 +228,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
object
ConfigUtilsTest
{
def
writeTemp
(
text
:
String
,
extension
:
String
)
:
File
=
{
val
file
=
File
.
createTempFile
(
"TestConfigUtils."
,
extension
)
file
.
deleteOnExit
()
val
w
=
new
PrintWriter
(
file
)
w
.
write
(
text
)
w
.
close
()
...
...
public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
View file @
2fdf69e7
...
...
@@ -39,6 +39,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records
.
header
shouldBe
Nil
val
tempFile
=
File
.
createTempFile
(
"region"
,
".bed"
)
tempFile
.
deleteOnExit
()
records
.
writeToFile
(
tempFile
)
BedRecordList
.
fromFile
(
tempFile
)
shouldBe
records
tempFile
.
delete
()
...
...
@@ -50,6 +51,7 @@ class BedRecordListTest extends TestNGSuite with Matchers {
records
.
header
shouldBe
BedRecordListTest
.
ucscHeader
.
split
(
"\n"
).
toList
val
tempFile
=
File
.
createTempFile
(
"region"
,
".bed"
)
tempFile
.
deleteOnExit
()
records
.
writeToFile
(
tempFile
)
BedRecordList
.
fromFile
(
tempFile
)
shouldBe
records
tempFile
.
delete
()
...
...
@@ -129,13 +131,6 @@ class BedRecordListTest extends TestNGSuite with Matchers {
list
.
scatter
(
100
).
allRecords
.
size
shouldBe
15
list
.
scatter
(
100
).
length
shouldBe
1500
}
@AfterClass
def
end
:
Unit
=
{
BedRecordListTest
.
bedFile
.
delete
()
BedRecordListTest
.
corruptBedFile
.
delete
()
BedRecordListTest
.
bedFileUcscHeader
.
delete
()
}
}
object
BedRecordListTest
{
...
...
@@ -149,6 +144,9 @@ object BedRecordListTest {
|chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399 0,3601"""
.
stripMargin
val
bedFile
=
File
.
createTempFile
(
"regions"
,
".bed"
)
bedFile
.
deleteOnExit
()
val
corruptBedFile
=
File
.
createTempFile
(
"regions"
,
".bed"
)
corruptBedFile
.
deleteOnExit
()
val
bedFileUcscHeader
=
File
.
createTempFile
(
"regions"
,
".bed"
)
bedFileUcscHeader
.
deleteOnExit
()
}
\ No newline at end of file
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