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biopet.biopet
Commits
3223c73b
Commit
3223c73b
authored
Mar 09, 2015
by
bow
Browse files
Update unit test for Gentrap
parent
9c5f43ad
Changes
1
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Inline
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public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
3223c73b
...
...
@@ -7,6 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.pipelines.gentrap.scripts.AggrBaseCount
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
...
...
@@ -110,7 +111,6 @@ class GentrapTest extends TestNGSuite with Matchers {
gentrap
.
script
()
val
functions
=
gentrap
.
functions
.
groupBy
(
_
.
getClass
)
val
numSamples
=
sampleConfig
(
"samples"
).
size
val
numLibPerSample
=
sampleConfig
(
"samples"
).
values
.
toSeq
.
head
(
"libraries"
).
size
functions
(
classOf
[
Gsnap
]).
size
should
be
>=
1
...
...
@@ -118,6 +118,51 @@ class GentrapTest extends TestNGSuite with Matchers {
gentrap
.
functions
.
collect
{
case
x
:
HtseqCount
=>
x
.
output
.
toString
.
endsWith
(
".fragments_per_gene"
)
}.
size
shouldBe
numSamples
}
if
(
expMeasures
.
contains
(
"fragments_per_exon"
))
{
gentrap
.
functions
.
collect
{
case
x
:
HtseqCount
=>
x
.
output
.
toString
.
endsWith
(
".fragments_per_exon"
)
}.
size
shouldBe
numSamples
}
if
(
expMeasures
.
contains
(
"bases_per_gene"
))
{
gentrap
.
functions
.
collect
{
case
x
:
AggrBaseCount
=>
x
.
output
.
toString
.
endsWith
(
".bases_per_gene"
)
}.
size
shouldBe
numSamples
}
if
(
expMeasures
.
contains
(
"bases_per_exon"
))
{
gentrap
.
functions
.
collect
{
case
x
:
AggrBaseCount
=>
x
.
output
.
toString
.
endsWith
(
".bases_per_exon"
)
}.
size
shouldBe
numSamples
}
if
(
expMeasures
.
contains
(
"cufflinks_strict"
))
{
gentrap
.
functions
.
collect
{
case
x
:
Cufflinks
=>
x
.
outputGenesFpkm
.
getParentFile
.
toString
.
endsWith
(
"cufflinks_strict"
)
case
x
:
Ln
=>
x
.
output
.
toString
.
endsWith
(
".genes_fpkm_cufflinks_strict"
)
||
x
.
output
.
toString
.
endsWith
(
".isoforms_fpkm_cufflinks_strict"
)
}
.
count
(
identity
)
shouldBe
numSamples
*
3
// three types of jobs per sample
}
if
(
expMeasures
.
contains
(
"cufflinks_guided"
))
{
gentrap
.
functions
.
collect
{
case
x
:
Cufflinks
=>
x
.
outputGenesFpkm
.
getParentFile
.
toString
.
endsWith
(
"cufflinks_guided"
)
case
x
:
Ln
=>
x
.
output
.
toString
.
endsWith
(
".genes_fpkm_cufflinks_guided"
)
||
x
.
output
.
toString
.
endsWith
(
".isoforms_fpkm_cufflinks_guided"
)
}
.
count
(
identity
)
shouldBe
numSamples
*
3
// three types of jobs per sample
}
if
(
expMeasures
.
contains
(
"cufflinks_blind"
))
{
gentrap
.
functions
.
collect
{
case
x
:
Cufflinks
=>
x
.
outputGenesFpkm
.
getParentFile
.
toString
.
endsWith
(
"cufflinks_blind"
)
case
x
:
Ln
=>
x
.
output
.
toString
.
endsWith
(
".genes_fpkm_cufflinks_blind"
)
||
x
.
output
.
toString
.
endsWith
(
".isoforms_fpkm_cufflinks_blind"
)
}
.
count
(
identity
)
shouldBe
numSamples
*
3
// three types of jobs per sample
}
}
// remove temporary run directory all tests in the class have been run
...
...
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