From 02177ff7b078d02caff27f5c90adfcf28121c73f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 15:50:25 +0100
Subject: [PATCH] Moved summary methods to general cutadept
---
.../sasc/biopet/extensions/Cutadapt.scala | 42 +++++++++++++++-
.../biopet/pipelines/flexiprep/Cutadapt.scala | 48 +------------------
2 files changed, 42 insertions(+), 48 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index e7a5a319e..ccf56efc8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -15,12 +15,16 @@
*/
package nl.lumc.sasc.biopet.extensions
+import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
-class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
+import scala.collection.mutable
+import scala.io.Source
+
+class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
@Input(doc = "Input fastq file")
var fastq_input: File = _
@@ -58,4 +62,40 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
required(fastq_input) +
required("--output", fastq_output) +
" > " + required(stats_output)
+
+ 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.toMap
+ )
+ }
+
+ 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()
}
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 e9f6bd492..dafbf8069 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
@@ -15,21 +15,11 @@
*/
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
-import org.broadinstitute.gatk.utils.commandline.{ Input }
-
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import scala.collection.mutable
-class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) with Summarizable {
+class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
var fastqc: Fastqc = _
override def beforeCmd() {
@@ -50,42 +40,6 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
Ln(this, fastq_input, fastq_output, relative = true).cmd
}
}
-
- 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.toMap
- )
- }
-
- 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()
}
object Cutadapt {
--
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