From 9fe0e57a670ebd8f5fa8f0ecde9003152f333bfb Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 6 Feb 2015 14:42:32 +0100
Subject: [PATCH] Parse module status in Flexiprep FastQC wrapper
---
.../biopet/pipelines/flexiprep/Fastqc.scala | 31 ++++++++++++-------
.../pipelines/flexiprep/FastqcV0101Test.scala | 8 +++++
2 files changed, 27 insertions(+), 12 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 196ce03fd..5e2fc66dd 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -34,6 +34,8 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
*/
class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
+ protected case class FastQCModule(name: String, status: String, lines: Seq[String])
+
/** Default FastQC output directory containing actual results */
// this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
def outputDir: File = new File(output.getAbsolutePath.stripSuffix(".zip"))
@@ -47,11 +49,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
*
* @return Mapping of FastQC module names and its contents as array of strings (one item per line)
* @throws FileNotFoundException if the FastQC data file can not be found.
- * @throws IllegalStateException if the module mapping is empty.
+ * @throws IllegalStateException if the module lines have no content or mapping is empty.
*/
@throws(classOf[FileNotFoundException])
@throws(classOf[IllegalStateException])
- def qcModules: Map[String, Array[String]] = {
+ def qcModules: Map[String, FastQCModule] = {
val fqModules = Source.fromFile(dataFile)
// drop all the characters before the first module delimiter (i.e. '>>')
@@ -64,14 +66,18 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
.map {
case (modString) =>
// module name is in the first line, without '>>' and before the tab character
- val modName = modString
- // so we take all characters in the first line
- .takeWhile(_ != '\n')
- // and drop all characters that equals '>'
+ val Array(firstLine, otherLines) = modString
+ // drop all '>>' character (start of module)
.dropWhile(_ == '>')
- // and take all characters before the tab
- .takeWhile(_ != '\t')
- modName -> modString.split('\n')
+ // split first line and others
+ .split("\n", 2)
+ // and slice them
+ .slice(0, 2)
+ // extract module name and module status
+ val Array(modName, modStatus) = firstLine
+ .split("\t", 2)
+ .slice(0, 2)
+ modName -> FastQCModule(modName, modStatus, otherLines.split("\n").toSeq)
}
.toMap
@@ -89,6 +95,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
@throws(classOf[NoSuchElementException])
def encoding: String =
qcModules("Basic Statistics")
+ .lines
.dropWhile(!_.startsWith("Encoding"))
.head
.stripPrefix("Encoding\t")
@@ -117,10 +124,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
}
val found = qcModules.get("Overrepresented sequences") match {
- case None => Array.empty[String]
- case Some(modLines) =>
+ case None => Seq.empty[String]
+ case Some(qcModule) =>
for (
- line <- modLines if !(line.startsWith("#") || line.startsWith(">"));
+ line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
values = line.split("\t") if values.size >= 4
) yield values(3)
}
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
index b9b922f4c..0951bea84 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
@@ -53,6 +53,14 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
fqc.qcModules.keySet should contain("Kmer Content")
}
+ @Test def testSingleQcModule() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.qcModules("Basic Statistics").name should ===("Basic Statistics")
+ fqc.qcModules("Basic Statistics").status should ===("pass")
+ fqc.qcModules("Basic Statistics").lines.size shouldBe 8
+ }
+
@Test def testEncoding() = {
val fqc = new Fastqc(null)
fqc.output = outputv0101
--
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