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biopet.biopet
Commits
bb72a164
Commit
bb72a164
authored
Aug 17, 2016
by
Peter van 't Hof
Browse files
Adding more testing for vep summary parsing
parent
77d657ac
Changes
2
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biopet-extensions/src/test/resources/vep.failed.metrics
0 → 100644
View file @
bb72a164
[VEP run statistics]
VEP version (API) 82 (82)
Cache/Database /usr/local/Genomes/H.Sapiens/GRCh37/annotation/vep/homo_sapiens_merged/81_GRCh37
Species homo_sapiens
Command line options -i /exports/sasc/pjvan_thof/toucan_test/output/chunk/chr17_GL000204_random-0-81310/chr17_GL000204_random-0-81310.vcf.gz -o /exports/sasc/pjvan_thof/toucan_test/output/chunk/chr17_GL000204_random-0-81310/chr17_GL000204_random-0-81310.vep.vcf -v --everything --stats_text --cache --vcf --allow_non_variant --merged --species homo_sapiens --assembly GRCh37 --dir /usr/local/Genomes/H.Sapiens/GRCh37/annotation/vep --fasta /usr/local/Genomes/H.Sapiens/GRCh37/annotation/vep/reference.fa --fork 2 --cache_version 81 --port 3337 --db_version 81 --failed 1
Start time 2016-08-17 13:44:42
End time 2016-08-17 13:44:42
Run time 0 seconds
Input file (format) /exports/sasc/pjvan_thof/toucan_test/output/chunk/chr17_GL000204_random-0-81310/chr17_GL000204_random-0-81310.vcf.gz (VCF)
Output file /exports/sasc/pjvan_thof/toucan_test/output/chunk/chr17_GL000204_random-0-81310/chr17_GL000204_random-0-81310.vep.vcf [text]
[General statistics]
Lines of input read 413
Variants processed
Variants remaining after filtering
Lines of output written
Novel / existing variants -
Overlapped genes
Overlapped transcripts
Overlapped regulatory features -
[Variant classes]
[Consequences (most severe)]
[Consequences (all)]
[Coding consequences]
[SIFT summary]
[PolyPhen summary]
[Variants by chromosome]
[Position in protein]
\ No newline at end of file
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
View file @
bb72a164
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
java.nio.file.Paths
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
...
...
@@ -46,4 +47,26 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers {
}
@Test
def
testFailedSummaryStats
=
{
val
file
=
new
File
(
Paths
.
get
(
getClass
.
getResource
(
"/vep.failed.metrics"
).
toURI
).
toString
)
val
vep
=
new
VariantEffectPredictor
(
null
)
val
stats
=
vep
.
parseStatsFile
(
file
)
}
@Test
def
testMergeFailSuccess
:
Unit
=
{
val
file1
=
new
File
(
Paths
.
get
(
getClass
.
getResource
(
"/vep.metrics"
).
toURI
).
toString
)
val
vep1
=
new
VariantEffectPredictor
(
null
)
val
stats1
=
vep1
.
parseStatsFile
(
file1
)
val
file2
=
new
File
(
Paths
.
get
(
getClass
.
getResource
(
"/vep.failed.metrics"
).
toURI
).
toString
)
val
vep2
=
new
VariantEffectPredictor
(
null
)
val
stats2
=
vep2
.
parseStatsFile
(
file2
)
ConfigUtils
.
mergeMaps
(
stats1
,
stats2
,
vep1
.
resolveSummaryConflict
)
ConfigUtils
.
mergeMaps
(
stats2
,
stats1
,
vep1
.
resolveSummaryConflict
)
}
}
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