diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 5fe30c554d3c9ba40efb687629d50fff1c6a235c..54a23127c6037e115e5586c70a6b206eb277cd13 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -93,12 +93,12 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
- else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
+ else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, output directory cannot be created")
inputFiles.foreach { i =>
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
- if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absulute path: ${i.file}")
+ if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
}
functions.filter(_.jobOutputFile == null).foreach(f => {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 42f504e191f205782e861a463adb0ad975332f45..97b4c74134a59ce94fea03ce0e843a5b6ee3adbc 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -17,16 +17,20 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
+import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.utils.tryToParseNumber
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import scala.io.Source
+
/**
* Extension for VariantEffectPredictor
* Created by ahbbollen on 15-1-15.
*/
-class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
executable = config("exe", submodule = "perl", default = "perl")
var vepScript: String = config("vep_script")
@@ -48,7 +52,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var everything: Boolean = config("everything", default = false)
var force: Boolean = config("force", default = false)
var no_stats: Boolean = config("no_stats", default = false)
- var stats_text: Boolean = config("stats_text", default = false)
+ var stats_text: Boolean = config("stats_text", default = true)
var html: Boolean = config("html", default = false)
var cache: Boolean = config("cache", default = false)
var humdiv: Boolean = config("humdiv", default = false)
@@ -254,4 +258,47 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--buffer_size", buffer_size) +
optional("--failed", failed)
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = {
+ if (stats_text) {
+ val stats_file: File = new File(output.getAbsolutePath + "_summary.txt")
+ parseStatsFile(stats_file)
+ } else {
+ Map()
+ }
+ }
+
+ def parseStatsFile(file: File): Map[String, Any] = {
+ val contents = Source.fromFile(file).getLines().toList
+ val headers = getHeadersFromStatsFile(contents)
+ headers.foldLeft(Map.empty[String, Any])((acc, x) => acc + (x.replace(" ", "_") -> getBlockFromStatsFile(contents, x)))
+ }
+
+ def getBlockFromStatsFile(contents: List[String], header: String): Map[String, Any] = {
+ var inBlock = false
+ var theMap: Map[String, Any] = Map()
+ for (x <- contents) {
+ val stripped = x.stripPrefix("[").stripSuffix("]")
+ if (stripped == header) {
+ inBlock = true
+ } else {
+ if (inBlock) {
+ val key = stripped.split('\t').head.replace(" ", "_")
+ val value = stripped.split('\t').last
+ theMap ++= Map(key -> tryToParseNumber(value, fallBack = true).getOrElse(value))
+ }
+ }
+ if (stripped == "") {
+ inBlock = false
+ }
+ }
+ theMap
+ }
+
+ def getHeadersFromStatsFile(contents: List[String]): List[String] = {
+ // block headers are of format '[block]'
+ contents.filter(_.startsWith("[")).filter(_.endsWith("]")).map(_.stripPrefix("[")).map(_.stripSuffix("]"))
+ }
+
}
diff --git a/public/biopet-extensions/src/test/resources/vep.metrics b/public/biopet-extensions/src/test/resources/vep.metrics
new file mode 100644
index 0000000000000000000000000000000000000000..c036c2b7dae5017c995132e3e2dd35d7d9cbcc13
--- /dev/null
+++ b/public/biopet-extensions/src/test/resources/vep.metrics
@@ -0,0 +1,349 @@
+[VEP run statistics]
+VEP version (API) 77 (77)
+Cache/Database /usr/local/Genomes/H.Sapiens/hg19/vep_cache_75/homo_sapiens/75
+Species homo_sapiens
+Command line options -i test.vcf -o test.vep.vcf -v --everything --stats_text --cache --vcf --allow_non_variant --species homo_sapiens --dir /usr/local/Genomes/H.Sapiens/hg19/vep_cache_75 --fasta /usr/local/Genomes/H.Sapiens/hg19/vep_cache_75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --fork 2 --cache_version 75 --db_version 75 --failed 1 --offline
+Start time 2016-03-03 14:37:44
+End time 2016-03-03 14:37:54
+Run time 10 seconds
+Input file (format) test.vcf (VCF)
+Output file test.vep.vcf [text]
+
+[General statistics]
+Lines of input read 1000
+Variants processed 874
+Variants remaining after filtering 874
+Lines of output written 874
+Novel / existing variants 105 (12.0%) / 769 (88.0%)
+Overlapped genes 132
+Overlapped transcripts 661
+Overlapped regulatory features 164
+
+[Variant classes]
+insertion 29
+deletion 51
+SNV 794
+
+[Consequences (most severe)]
+splice_donor_variant 3
+frameshift_variant 1
+inframe_insertion 2
+inframe_deletion 1
+missense_variant 39
+splice_region_variant 11
+synonymous_variant 46
+5_prime_UTR_variant 19
+3_prime_UTR_variant 36
+non_coding_transcript_exon_variant 95
+intron_variant 518
+upstream_gene_variant 48
+downstream_gene_variant 27
+intergenic_variant 28
+
+[Consequences (all)]
+splice_donor_variant 6
+frameshift_variant 2
+inframe_insertion 15
+inframe_deletion 6
+missense_variant 101
+splice_region_variant 60
+synonymous_variant 173
+coding_sequence_variant 1
+5_prime_UTR_variant 33
+3_prime_UTR_variant 108
+non_coding_transcript_exon_variant 279
+intron_variant 3311
+NMD_transcript_variant 437
+non_coding_transcript_variant 1102
+upstream_gene_variant 1486
+downstream_gene_variant 1779
+TF_binding_site_variant 12
+feature_elongation 97
+regulatory_region_variant 253
+feature_truncation 278
+intergenic_variant 28
+
+[Coding consequences]
+frameshift_variant 2
+inframe_insertion 15
+inframe_deletion 6
+missense_variant 101
+synonymous_variant 173
+coding_sequence_variant 1
+
+[SIFT summary]
+deleterious 22
+tolerated 76
+
+[PolyPhen summary]
+possibly damaging 7
+unknown 12
+probably damaging 12
+benign 70
+
+[Variants by chromosome]
+1 874
+
+[Distribution of variants on chromosome 1]
+0 225
+1 407
+2 242
+3 0
+4 0
+5 0
+6 0
+7 0
+8 0
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 0
+16 0
+17 0
+18 0
+19 0
+20 0
+21 0
+22 0
+23 0
+24 0
+25 0
+26 0
+27 0
+28 0
+29 0
+30 0
+31 0
+32 0
+33 0
+34 0
+35 0
+36 0
+37 0
+38 0
+39 0
+40 0
+41 0
+42 0
+43 0
+44 0
+45 0
+46 0
+47 0
+48 0
+49 0
+50 0
+51 0
+52 0
+53 0
+54 0
+55 0
+56 0
+57 0
+58 0
+59 0
+60 0
+61 0
+62 0
+63 0
+64 0
+65 0
+66 0
+67 0
+68 0
+69 0
+70 0
+71 0
+72 0
+73 0
+74 0
+75 0
+76 0
+77 0
+78 0
+79 0
+80 0
+81 0
+82 0
+83 0
+84 0
+85 0
+86 0
+87 0
+88 0
+89 0
+90 0
+91 0
+92 0
+93 0
+94 0
+95 0
+96 0
+97 0
+98 0
+99 0
+100 0
+101 0
+102 0
+103 0
+104 0
+105 0
+106 0
+107 0
+108 0
+109 0
+110 0
+111 0
+112 0
+113 0
+114 0
+115 0
+116 0
+117 0
+118 0
+119 0
+120 0
+121 0
+122 0
+123 0
+124 0
+125 0
+126 0
+127 0
+128 0
+129 0
+130 0
+131 0
+132 0
+133 0
+134 0
+135 0
+136 0
+137 0
+138 0
+139 0
+140 0
+141 0
+142 0
+143 0
+144 0
+145 0
+146 0
+147 0
+148 0
+149 0
+150 0
+151 0
+152 0
+153 0
+154 0
+155 0
+156 0
+157 0
+158 0
+159 0
+160 0
+161 0
+162 0
+163 0
+164 0
+165 0
+166 0
+167 0
+168 0
+169 0
+170 0
+171 0
+172 0
+173 0
+174 0
+175 0
+176 0
+177 0
+178 0
+179 0
+180 0
+181 0
+182 0
+183 0
+184 0
+185 0
+186 0
+187 0
+188 0
+189 0
+190 0
+191 0
+192 0
+193 0
+194 0
+195 0
+196 0
+197 0
+198 0
+199 0
+200 0
+201 0
+202 0
+203 0
+204 0
+205 0
+206 0
+207 0
+208 0
+209 0
+210 0
+211 0
+212 0
+213 0
+214 0
+215 0
+216 0
+217 0
+218 0
+219 0
+220 0
+221 0
+222 0
+223 0
+224 0
+225 0
+226 0
+227 0
+228 0
+229 0
+230 0
+231 0
+232 0
+233 0
+234 0
+235 0
+236 0
+237 0
+238 0
+239 0
+240 0
+241 0
+242 0
+243 0
+244 0
+245 0
+246 0
+247 0
+248 0
+249 0
+
+[Position in protein]
+00-10% 29
+10-20% 63
+20-30% 34
+30-40% 20
+40-50% 23
+50-60% 25
+60-70% 31
+70-80% 11
+80-90% 32
+90-100% 30
diff --git a/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..54e5ef6733edd578653940eaa92eb77e7ea0f3c0
--- /dev/null
+++ b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
@@ -0,0 +1,37 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by ahbbollen on 3-3-16.
+ */
+class VariantEffectPredictorTest extends TestNGSuite with Matchers {
+
+
+ @Test
+ def testSummaryStats = {
+ val file = new File(Paths.get(getClass.getResource("/vep.metrics").toURI).toString)
+
+ val vep = new VariantEffectPredictor(null)
+ val stats = vep.parseStatsFile(file)
+
+ stats.contains("VEP_run_statistics") shouldBe true
+ stats.contains("General_statistics") shouldBe true
+ stats.contains("Consequences_(most_severe)") shouldBe true
+ stats.contains("Consequences_(all)") shouldBe true
+ stats.contains("Coding_consequences") shouldBe true
+ stats.contains("SIFT_summary") shouldBe true
+ stats.contains("PolyPhen_summary") shouldBe true
+ stats.contains("Variants_by_chromosome") shouldBe true
+ stats.contains("Distribution_of_variants_on_chromosome_1") shouldBe true
+ stats.contains("Position_in_protein") shouldBe true
+
+
+ }
+
+}
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 7464366e69387664569796b1b523191abec7bb80..1ccb0ea95fedc96d6e967e073ef80a6c3abc0195 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -68,6 +68,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
vep.output = new File(outputDir, inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf")
vep.isIntermediate = true
add(vep)
+ addSummarizable(vep, "variant_effect_predictor")
val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output