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Mirrors
biopet.biopet
Commits
18c79226
Commit
18c79226
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Move unit testing variantcalling to public
parent
76381e8c
Changes
2
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
deleted
100644 → 0
View file @
76381e8c
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
/**
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaVariantcallingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
ShivaVariantcalling
=
{
new
ShivaVariantcalling
()
{
override
def
configNamespace
=
"shivavariantcalling"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcallingTest
.
config
))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
}
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
val
bool
=
Array
(
true
,
false
)
(
for
(
bams
<-
0
to
2
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
haplotypeCallerGvcf
<-
bool
;
haplotypeCallerAllele
<-
bool
;
unifiedGenotyperAllele
<-
bool
;
unifiedGenotyper
<-
bool
;
haplotypeCaller
<-
bool
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
)
).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
def
testShivaVariantcalling
(
bams
:
Int
,
raw
:
Boolean
,
bcftools
:
Boolean
,
bcftools_singlesample
:
Boolean
,
unifiedGenotyper
:
Boolean
,
haplotypeCaller
:
Boolean
,
haplotypeCallerGvcf
:
Boolean
,
haplotypeCallerAllele
:
Boolean
,
unifiedGenotyperAllele
:
Boolean
)
=
{
val
callers
:
ListBuffer
[
String
]
=
ListBuffer
()
if
(
raw
)
callers
.
append
(
"raw"
)
if
(
bcftools
)
callers
.
append
(
"bcftools"
)
if
(
bcftools_singlesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
unifiedGenotyper
)
callers
.
append
(
"unifiedgenotyper"
)
if
(
haplotypeCallerGvcf
)
callers
.
append
(
"haplotypecaller_gvcf"
)
if
(
haplotypeCallerAllele
)
callers
.
append
(
"haplotypecaller_allele"
)
if
(
unifiedGenotyperAllele
)
callers
.
append
(
"unifiedgenotyper_allele"
)
if
(
haplotypeCaller
)
callers
.
append
(
"haplotypecaller"
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
haplotypeCaller
&&
!
unifiedGenotyper
&&
!
haplotypeCallerGvcf
&&
!
haplotypeCallerAllele
&&
!
unifiedGenotyperAllele
&&
!
bcftools_singlesample
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
}
if
(!
illegalArgumentException
)
{
pipeline
.
script
()
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
1
+
(
if
(
raw
)
1
else
0
)
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
//pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfFilter
])
shouldBe
(
if
(
raw
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
HaplotypeCaller
])
shouldBe
(
if
(
haplotypeCaller
)
1
else
0
)
+
(
if
(
haplotypeCallerAllele
)
1
else
0
)
+
(
if
(
haplotypeCallerGvcf
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
UnifiedGenotyper
])
shouldBe
(
if
(
unifiedGenotyper
)
1
else
0
)
+
(
if
(
unifiedGenotyperAllele
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
)
}
}
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
ShivaVariantcallingTest
.
outputDir
)
}
}
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
outputDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"cache"
->
true
,
"dir"
->
"test"
,
"vep_script"
->
"test"
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"input_alleles"
->
"test.vcf.gz"
)
}
\ No newline at end of file
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
18c79226
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetPipe
import
nl.lumc.sasc.biopet.extensions.Freebayes
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
/**
* Test c
lass for
[[
ShivaVariantcalling
]]
*
* Created by pjvan_thof on 3/2/15.
*/
* C
lass for
testing
ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaVariantcallingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
ShivaVariantcalling
=
{
new
ShivaVariantcalling
{
new
ShivaVariantcalling
()
{
override
def
configNamespace
=
"shivavariantcalling"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcallingTest
.
config
))
qSettings
=
new
QSettings
...
...
@@ -50,14 +43,19 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
val
bool
=
Array
(
true
,
false
)
(
for
(
bams
<-
0
to
3
;
bams
<-
0
to
2
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftoolsSinglesample
<-
bool
;
freebayes
<-
bool
;
varscanCnsSinglesample
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftoolsSinglesample
,
freebayes
,
varscanCnsSinglesample
)).
toArray
bcftools_singlesample
<-
bool
;
haplotypeCallerGvcf
<-
bool
;
haplotypeCallerAllele
<-
bool
;
unifiedGenotyperAllele
<-
bool
;
unifiedGenotyper
<-
bool
;
haplotypeCaller
<-
bool
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
)
).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
...
...
@@ -65,12 +63,22 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
raw
:
Boolean
,
bcftools
:
Boolean
,
bcftoolsSinglesample
:
Boolean
,
unifiedGenotyper
:
Boolean
,
haplotypeCaller
:
Boolean
,
haplotypeCallerGvcf
:
Boolean
,
haplotypeCallerAllele
:
Boolean
,
unifiedGenotyperAllele
:
Boolean
,
freebayes
:
Boolean
,
varscanCnsSinglesample
:
Boolean
)
=
{
val
callers
:
ListBuffer
[
String
]
=
ListBuffer
()
if
(
raw
)
callers
.
append
(
"raw"
)
if
(
bcftools
)
callers
.
append
(
"bcftools"
)
if
(
bcftoolsSinglesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
unifiedGenotyper
)
callers
.
append
(
"unifiedgenotyper"
)
if
(
haplotypeCallerGvcf
)
callers
.
append
(
"haplotypecaller_gvcf"
)
if
(
haplotypeCallerAllele
)
callers
.
append
(
"haplotypecaller_allele"
)
if
(
unifiedGenotyperAllele
)
callers
.
append
(
"unifiedgenotyper_allele"
)
if
(
haplotypeCaller
)
callers
.
append
(
"haplotypecaller"
)
if
(
freebayes
)
callers
.
append
(
"freebayes"
)
if
(
varscanCnsSinglesample
)
callers
.
append
(
"varscan_cns_singlesample"
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
...
...
@@ -78,15 +86,17 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftoolsSinglesample
&&
!
freebayes
&&
!
varscanCnsSinglesample
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
haplotypeCaller
&&
!
unifiedGenotyper
&&
!
haplotypeCallerGvcf
&&
!
haplotypeCallerAllele
&&
!
unifiedGenotyperAllele
&&
!
bcftoolsSinglesample
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
init
()
pipeline
.
script
()
}
if
(!
illegalArgumentException
)
{
pipeline
.
init
()
pipeline
.
script
()
val
pipesJobs
=
pipeline
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetPipe
]).
flatMap
(
_
.
asInstanceOf
[
BiopetPipe
].
pipesJobs
)
...
...
@@ -97,15 +107,23 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipesJobs
.
count
(
_
.
isInstanceOf
[
Freebayes
])
shouldBe
(
if
(
freebayes
)
1
else
0
)
pipesJobs
.
count
(
_
.
isInstanceOf
[
MpileupToVcf
])
shouldBe
(
if
(
raw
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfFilter
])
shouldBe
(
if
(
raw
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
HaplotypeCaller
])
shouldBe
(
if
(
haplotypeCaller
)
1
else
0
)
+
(
if
(
haplotypeCallerAllele
)
1
else
0
)
+
(
if
(
haplotypeCallerGvcf
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
UnifiedGenotyper
])
shouldBe
(
if
(
unifiedGenotyper
)
1
else
0
)
+
(
if
(
unifiedGenotyperAllele
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
)
}
}
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
ShivaVariantcallingTest
.
outputDir
)
}
}
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
private
def
inputTouch
(
name
:
String
)
:
File
=
{
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
...
...
@@ -132,12 +150,9 @@ object ShivaVariantcallingTest {
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
"freebayes"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"rscript"
->
Map
(
"exe"
->
"test"
),
"exe"
->
"test"
,
"varscan_jar"
->
"test"
"input_alleles"
->
"test.vcf.gz"
)
}
\ No newline at end of file
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