From 0eed5996af962b39b0e2ae3cf519a52b4c90d011 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 11:32:27 +0100
Subject: [PATCH] Added new summary to cutadept
---
.../biopet/pipelines/flexiprep/Cutadapt.scala | 48 +++++++++++++++++--
1 file changed, 43 insertions(+), 5 deletions(-)
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 9aaca5f66..15996cbe7 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
@@ -15,6 +15,8 @@
*/
package nl.lumc.sasc.biopet.pipelines.flexiprep
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+
import scala.io.Source
import nl.lumc.sasc.biopet.extensions.Ln
@@ -25,9 +27,9 @@ import scalaz._, Scalaz._
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import scala.collection.mutable.Map
+import scala.collection.mutable
-class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
+class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) with Summarizable {
var fastqc: Fastqc = _
override def beforeCmd() {
@@ -49,14 +51,50 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
}
}
+ def summaryData: 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, 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) => adapter_stats += (adapter -> count.toInt)
+ case _ =>
+ }
+ }
+
+ Map("version" -> getVersion,
+ "num_reads_affected" -> stats("trimmed"),
+ "num_reads_discarded_too_short" -> stats("tooshort"),
+ "num_reads_discarded_too_long" -> stats("toolong"),
+ "adapters" -> adapter_stats
+ )
+ }
+
+ override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+ (v1, v2) match {
+ case (v1: Int, v2: Int) => v1 + v2
+ case _ => v1
+ }
+ }
+
+ def summaryFiles: Map[String, File] = Map("input" -> fastq_input, "output" -> fastq_output)
+
def getSummary: Json = {
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
- var stats: Map[String, Int] = Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
- var adapter_stats: Map[String, Int] = Map()
+ var stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
+ var adapter_stats: mutable.Map[String, Int] = mutable.Map()
if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines) {
line match {
@@ -88,7 +126,7 @@ object Cutadapt {
var affected = 0
var tooShort = 0
var tooLong = 0
- var adapter_stats: Map[String, Int] = Map()
+ var adapter_stats: mutable.Map[String, Int] = mutable.Map()
for (json <- jsons) {
affected += json.field("num_reads_affected").get.numberOrZero.toInt
--
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