diff --git a/biopet-extensions/src/test/resources/vep.failed.metrics b/biopet-extensions/src/test/resources/vep.failed.metrics new file mode 100644 index 0000000000000000000000000000000000000000..b722714c7a49f7c77ab9393fee72a50a45677a69 --- /dev/null +++ b/biopet-extensions/src/test/resources/vep.failed.metrics @@ -0,0 +1,36 @@ +[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 diff --git a/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala b/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala index e51103de2a4908ea299a8872c4eb54d3d6fc63fc..016608275daa3cb0abace7ab6e821bb09b225aac 100644 --- a/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala +++ b/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala @@ -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) + } + }