From 2a2a37fd6d5c5c420ee90e917dec807ac453387e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 27 Jul 2014 12:16:13 +0200
Subject: [PATCH] Function to get encoding of the fastq file, replaces python
script
---
.../sasc/biopet/function/fastq/Fastqc.scala | 30 +++++++++++++++++--
1 file changed, 28 insertions(+), 2 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index ca30614d1..d0ce249e0 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -1,6 +1,7 @@
package nl.lumc.sasc.biopet.function.fastq
import java.io.File
+import scala.io.Source
import scala.sys.process._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -32,8 +33,10 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
this.checkExecutable
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
- if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+ if (contaminants == null) {
+ val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+ contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+ }
}
override def versionCommand = executable + " --version"
@@ -51,6 +54,29 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
required("-o", output.getParent()) +
required(fastqfile)
}
+
+ def getDataBlock(name:String): Array[String] = { // Based on Fastqc v0.10.1
+ val outputDir = output.getName.stripSuffix(".zip")
+ val dataFile = new File(outputDir + "/fastqc_data.txt")
+ if (!dataFile.exists) return null
+ val data = Source.fromFile(dataFile).mkString
+ for (block <- data.split(">>END_MODULE\n")) {
+ val b = if (block.startsWith("##FastQC")) block.substring(block.indexOf("\n") + 1) else block
+ if (b.startsWith(">>" + name))
+ return for (line <- b.split("\n"))
+ yield line
+ }
+ return null
+ }
+
+ def getEncoding: String = {
+ val block = getDataBlock("Basic Statistics")
+ if (block == null) return null
+ for (line <- block
+ if (line.startsWith("Encoding")))
+ return line.stripPrefix("Encoding\t")
+ return null // Could be default Sanger with a warning in the log
+ }
}
object Fastqc {
--
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