Commit bb72a164 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding more testing for vep summary parsing

parent 77d657ac
[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
...@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions ...@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import import
import java.nio.file.Paths import java.nio.file.Paths
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test import org.testng.annotations.Test
...@@ -46,4 +47,26 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers { ...@@ -46,4 +47,26 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers {
} }
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)
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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