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biopet.biopet
Commits
052f9e11
Commit
052f9e11
authored
May 17, 2016
by
Peter van 't Hof
Browse files
Added mapping to gears testing
parent
75f13b0e
Changes
3
Hide whitespace changes
Inline
Side-by-side
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
052f9e11
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.kraken.Kraken
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
...
...
@@ -25,7 +26,7 @@ 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.
{
Before
Class
,
After
Class
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
After
Class
,
Before
Class
,
DataProvider
,
Test
}
/**
* Test class for [[Mapping]]
...
...
@@ -42,14 +43,15 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
}
}
def
paired
=
Array
(
true
,
false
)
def
chunks
=
Array
(
1
,
5
)
def
skipMarkDuplicates
=
Array
(
true
,
false
)
def
skipFlexipreps
=
Array
(
true
,
false
)
def
zipped
=
Array
(
true
,
false
)
def
unmappedToGears
=
false
@DataProvider
(
name
=
"mappingOptions"
)
def
mappingOptions
=
{
val
paired
=
Array
(
true
,
false
)
val
chunks
=
Array
(
1
,
5
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
val
skipFlexipreps
=
Array
(
true
,
false
)
val
zipped
=
Array
(
true
,
false
)
for
(
pair
<-
paired
;
chunk
<-
chunks
;
...
...
@@ -68,7 +70,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
"aligner"
->
aligner
,
"number_chunks"
->
chunks
,
"skip_markduplicates"
->
skipMarkDuplicate
,
"skip_flexiprep"
->
skipFlexiprep
"skip_flexiprep"
->
skipFlexiprep
,
"unmapped_to_gears"
->
unmappedToGears
),
Map
(
executables
.
toSeq
:
_
*
))
val
mapping
:
Mapping
=
initPipeline
(
map
)
...
...
@@ -85,6 +88,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
//Flexiprep
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Fastqc
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
4
else
2
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
(
if
(
unmappedToGears
)
1
else
0
)
}
val
outputDir
=
Files
.
createTempDir
()
...
...
@@ -133,6 +138,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
"bowtie2"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
,
"genome"
->
"test"
,
"hash"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
...
...
@@ -151,3 +158,13 @@ class MappingBowtie2Test extends AbstractTestMapping("bowtie2")
class
MappingStampyTest
extends
AbstractTestMapping
(
"stampy"
)
class
MappingGsnapTest
extends
AbstractTestMapping
(
"gsnap"
)
class
MappingTophatTest
extends
AbstractTestMapping
(
"tophat"
)
class
MappingGearsTest
extends
AbstractTestMapping
(
"bwa-mem"
)
{
override
def
unmappedToGears
=
true
override
def
paired
=
Array
(
true
)
override
def
chunks
=
Array
(
1
)
override
def
skipMarkDuplicates
=
Array
(
true
)
override
def
skipFlexipreps
=
Array
(
true
)
override
def
zipped
=
Array
(
true
)
}
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
052f9e11
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.kraken.Kraken
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
...
...
@@ -12,8 +13,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Created by pjvanthof on 15/05/16.
*/
* Created by pjvanthof on 15/05/16.
*/
trait
MultisampleMappingTestTrait
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
MultisampleMapping
=
{
new
MultisampleMapping
()
{
...
...
@@ -36,7 +37,7 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"mappingOptions"
)
def
mappingOptions
=
{
for
(
merge
<-
mergeStrategies
.
toArray
;
s1
<-
sample1
;
s2
<-
sample2
merge
<-
mergeStrategies
.
toArray
;
s1
<-
sample1
;
s2
<-
sample2
)
yield
Array
(
merge
,
s1
,
s2
)
}
...
...
@@ -76,13 +77,18 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MarkDuplicates
||
merge
==
MergeStrategy
.
PreProcessMarkDuplicates
))
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MergeSam
||
merge
==
MergeStrategy
.
PreProcessMergeSam
))
1
else
0
))
pipeline
.
samples
.
foreach
{
case
(
sampleName
,
sample
)
=>
if
(
merge
==
MergeStrategy
.
None
)
sample
.
bamFile
shouldBe
None
sample
.
summaryStats
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libraryId
,
library
)
=>
library
.
summaryStats
shouldBe
Map
()
}
pipeline
.
samples
.
foreach
{
case
(
sampleName
,
sample
)
=>
if
(
merge
==
MergeStrategy
.
None
)
sample
.
bamFile
shouldBe
None
sample
.
summaryStats
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libraryId
,
library
)
=>
library
.
summaryStats
shouldBe
Map
()
}
}
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
(
if
(
unmappedToGears
)
(
numberFastqLibs
+
numberSamples
)
else
0
)
pipeline
.
summarySettings
.
get
(
"merge_strategy"
)
shouldBe
Some
(
merge
.
toString
)
}
}
...
...
@@ -98,6 +104,13 @@ class MultisampleMappingNoSamplesTest extends MultisampleMappingTestTrait {
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingGearsTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
unmappedToGears
=
true
override
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
.
filter
(
_
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
}
class
MultisampleMappingBamTest
extends
MultisampleMappingTestTrait
{
override
def
sample1
=
Array
(
false
)
override
def
sample2
=
Array
(
false
)
...
...
@@ -168,6 +181,8 @@ object MultisampleMappingTestTrait {
"samtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
052f9e11
...
...
@@ -5,21 +5,21 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
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.gatk.
{
CombineVariants
,
GenotypeConcordance
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
GenotypeConcordance
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
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.
{
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
...
...
@@ -117,7 +117,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
(
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
+
(
roiBedFiles
++
ampliconBedFile
).
length
*
(
1
+
callers
.
size
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
+
(
roiBedFiles
++
ampliconBedFile
).
length
*
(
1
+
callers
.
size
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtNormalize
])
shouldBe
(
if
(
normalize
)
callers
.
size
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtDecompose
])
shouldBe
(
if
(
decompose
)
callers
.
size
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
GenotypeConcordance
])
shouldBe
(
if
(
referenceVcf
.
isDefined
)
1
+
callers
.
size
else
0
)
...
...
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