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biopet.biopet
Commits
36641e26
Commit
36641e26
authored
Feb 12, 2015
by
Peter van 't Hof
Browse files
Added 128 unit tests to mapping pipeline
parent
953e054c
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/mapping/pom.xml
View file @
36641e26
...
...
@@ -49,5 +49,17 @@
<artifactId>
BamMetrics
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.11
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
</dependencies>
</project>
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
0 → 100644
View file @
36641e26
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaSamse
,
BwaSampe
,
BwaAln
,
BwaMem
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MergeSamFiles
,
AddOrReplaceReadGroups
,
MarkDuplicates
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Sickle
import
nl.lumc.sasc.biopet.pipelines.flexiprep._
import
nl.lumc.sasc.biopet.tools.FastqSync
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
}
/**
* Created by pjvan_thof on 2/12/15.
*/
class
MappingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Mapping
=
{
new
Mapping
{
override
def
configName
=
"mapping"
override
def
globalConfig
=
new
Config
(
map
)
qSettings
=
new
QSettings
qSettings
.
runName
=
"test."
+
System
.
currentTimeMillis
}
}
@DataProvider
(
name
=
"mappingOptions"
,
parallel
=
true
)
def
mappingOptions
=
{
val
aligners
=
Array
(
"bwa"
,
"bwa-aln"
,
"star"
,
"bowtie"
)
val
paired
=
Array
(
true
,
false
)
val
chunks
=
Array
(
1
,
5
,
10
,
100
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
val
skipFlexipreps
=
Array
(
true
,
false
)
for
(
aligner
<-
aligners
;
pair
<-
paired
;
chunk
<-
chunks
;
skipMarkDuplicate
<-
skipMarkDuplicates
;
skipFlexiprep
<-
skipFlexipreps
)
yield
Array
(
aligner
,
pair
,
chunk
,
skipMarkDuplicate
,
skipFlexiprep
)
}
@Test
(
dataProvider
=
"mappingOptions"
)
def
testMapping
(
aligner
:
String
,
paired
:
Boolean
,
chunks
:
Int
,
skipMarkDuplicate
:
Boolean
,
skipFlexiprep
:
Boolean
)
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
MappingTest
.
outputDir
,
"aligner"
->
aligner
,
"number_chunks"
->
chunks
,
"skip_markduplicates"
->
skipMarkDuplicate
,
"skip_flexiprep"
->
skipFlexiprep
),
Map
(
MappingTest
.
excutables
.
toSeq
:
_
*
))
val
mapping
:
Mapping
=
initPipeline
(
map
)
mapping
.
input_R1
=
new
File
(
mapping
.
outputDir
,
"bla_R1.fq"
)
if
(
paired
)
mapping
.
input_R2
=
Some
(
new
File
(
mapping
.
outputDir
,
"bla_R2.fq"
))
mapping
.
sampleId
=
"1"
mapping
.
libId
=
"1"
mapping
.
script
()
//Flexiprep
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Fastqc
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
4
else
2
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Zcat
])
shouldBe
0
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SeqtkSeq
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Cutadapt
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
&&
!
skipFlexiprep
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Sickle
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
//aligners
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
((
if
(
aligner
==
"bwa"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaAln
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
2
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSampe
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
1
else
0
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSamse
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
0
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Star
])
shouldBe
((
if
(
aligner
==
"star"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Star
])
shouldBe
((
if
(
aligner
==
"star"
)
1
else
if
(
aligner
==
"star-2pass"
)
3
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Bowtie
])
shouldBe
((
if
(
aligner
==
"bowtie"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Stampy
])
shouldBe
((
if
(
aligner
==
"stampy"
)
1
else
0
)
*
chunks
)
// Sort sam or replace readgroup
val
sort
=
aligner
match
{
case
"bwa"
|
"bwa-aln"
|
"stampy"
=>
"sortsam"
case
"star"
|
"star-2pass"
|
"bowtie"
=>
"replacereadgroups"
case
_
=>
throw
new
IllegalArgumentException
(
"aligner: "
+
aligner
+
" does not exist"
)
}
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
((
if
(
sort
==
"sortsam"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
AddOrReplaceReadGroups
])
shouldBe
((
if
(
sort
==
"replacereadgroups"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
if
(
skipMarkDuplicate
&&
chunks
>
1
)
1
else
0
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
if
(
skipMarkDuplicate
)
0
else
1
)
}
}
object
MappingTest
{
val
outputDir
=
System
.
getProperty
(
"java.io.tmpdir"
)
+
File
.
separator
+
"flexiprep"
val
excutables
=
Map
(
"reference"
->
"test"
,
"seqstat"
->
Map
(
"exe"
->
"test"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
)
)
}
\ No newline at end of file
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