From 66bf4e3ff6e0f3a6c41c9a0f33c6001417bb468f Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 6 Mar 2015 19:29:26 +0100
Subject: [PATCH] Fix missing adapter name in flexiprep summary
---
.../biopet/pipelines/flexiprep/Cutadapt.scala | 35 ++++++++++++++++++-
1 file changed, 34 insertions(+), 1 deletion(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index dafbf8069..cac6bba92 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -15,8 +15,11 @@
*/
package nl.lumc.sasc.biopet.pipelines.flexiprep
-import nl.lumc.sasc.biopet.extensions.Ln
import java.io.File
+import scala.collection.mutable
+import scala.io.Source
+
+import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.core.config.Configurable
class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
@@ -31,6 +34,36 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
else if (default_clip_mode == "both") opt_anywhere ++= foundAdapters
}
+ override def summaryStats: Map[String, Any] = {
+ val trimR = """.*Trimmed reads: *(\d*) .*""".r
+ val tooShortR = """.*Too short reads: *(\d*) .*""".r
+ val tooLongR = """.*Too long reads: *(\d*) .*""".r
+ val adapterR = """Adapter '([C|T|A|G]*)'.*trimmed (\d*) times.""".r
+
+ val stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
+ val adapter_stats: mutable.Map[String, (String, Int)] = mutable.Map()
+
+ if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines) {
+ line match {
+ case trimR(m) => stats += ("trimmed" -> m.toInt)
+ case tooShortR(m) => stats += ("tooshort" -> m.toInt)
+ case tooLongR(m) => stats += ("toolong" -> m.toInt)
+ case adapterR(adapter, count) =>
+ val adapterName = fastqc.foundAdapters.find(_.seq == adapter) match {
+ case None => "unknown"
+ case Some(a) => a.name
+ }
+ adapter_stats += (adapter -> (adapterName, count.toInt))
+ case _ =>
+ }
+ }
+
+ Map("num_reads_affected" -> stats("trimmed"),
+ "num_reads_discarded_too_short" -> stats("tooshort"),
+ "num_reads_discarded_too_long" -> stats("toolong"),
+ "adapters" -> adapter_stats.toMap
+ )
+ }
override def cmdLine = {
if (opt_adapter.nonEmpty || opt_anywhere.nonEmpty || opt_front.nonEmpty) {
analysisName = getClass.getSimpleName
--
GitLab