From 6a492c14b52302cb4e3ffadcb61606501fd5bb60 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sat, 25 Oct 2014 23:30:15 +0200
Subject: [PATCH] Use DataProvider for testing multiple combinations
---
.../biopet/tools/ExtractAlignedFastq.scala | 19 +--
.../tools/ExtractAlignedFastqUnitTest.scala | 148 ++++++++++--------
2 files changed, 92 insertions(+), 75 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 3bce35461..df5e20100 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -5,13 +5,14 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
+
import scala.collection.mutable.{ Set => MSet }
import scala.collection.JavaConverters._
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMFileReader.QueryInterval
import htsjdk.samtools.SAMRecord
-import htsjdk.samtools.fastq.{BasicFastqWriter, FastqWriter, FastqReader, FastqRecord}
+import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
import htsjdk.tribble.Feature
import htsjdk.tribble.BasicFeature
@@ -19,6 +20,7 @@ import nl.lumc.sasc.biopet.core.ToolCommand
object ExtractAlignedFastq extends ToolCommand {
+ type FastqPair = (FastqRecord, FastqRecord)
/**
* Function to create iterator over features given input interval string
*
@@ -72,7 +74,7 @@ object ExtractAlignedFastq extends ToolCommand {
inAln: File,
commonSuffixLength: Int = 0,
readGroupIds: Set[String] = Set.empty[String]
- ): ((FastqRecord, FastqRecord) => Boolean) = {
+ ): (FastqPair => Boolean) = {
/** function to make interval queries for BAM files */
def makeQueryInterval(aln: SAMFileReader, feat: Feature): QueryInterval =
@@ -119,17 +121,16 @@ object ExtractAlignedFastq extends ToolCommand {
}
)
- (rec1: FastqRecord, rec2: FastqRecord) => rec2 match {
- case null => selected.contains(rec1.getReadHeader)
+ (pair: FastqPair) => pair._2 match {
+ case null => selected.contains(pair._1.getReadHeader)
case otherwise =>
- require (commonSuffixLength < rec1.getReadHeader.length)
- require (commonSuffixLength < rec2.getReadHeader.length)
- println(rec1.getReadHeader.dropRight(commonSuffixLength))
- selected.contains(rec1.getReadHeader.dropRight(commonSuffixLength))
+ require(commonSuffixLength < pair._1.getReadHeader.length)
+ require(commonSuffixLength < pair._2.getReadHeader.length)
+ selected.contains(pair._1.getReadHeader.dropRight(commonSuffixLength))
}
}
- def selectFastqReads(memFunc: (FastqRecord, FastqRecord) => Boolean,
+ def selectFastqReads(memFunc: FastqPair => Boolean,
inputFastq1: File,
outputFastq1: File,
inputFastq2: File = null,
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
index fbc639be5..638ca788e 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
+++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala
@@ -8,7 +8,7 @@ import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
+import org.testng.annotations.{ DataProvider, Test }
import htsjdk.samtools.fastq.FastqRecord
import htsjdk.tribble._
@@ -20,38 +20,20 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with Matchers {
private def resourceFile(p: String): File =
new File(Paths.get(getClass.getResource(p).toURI).toString)
- private def makeFeatures(features: (String, Int, Int)*): Seq[Feature] =
- features.map(x => new BasicFeature(x._1, x._2, x._3))
-
- private def makeFastqRecords(raws: (String, String, String, String)*): Seq[FastqRecord] =
- raws.map(x => new FastqRecord(x._1, x._2, x._3, x._4))
-
- val sBam01 = resourceFile("/single01.bam")
- val pBam01 = resourceFile("/paired01.bam")
-
- val sFastq1 = makeFastqRecords(
- ("r01", "A", "", "H"),
- ("r02", "T", "", "H"),
- ("r03", "G", "", "H"),
- ("r04", "C", "", "H"),
- ("r05", "AT", "", "HH")
- )
-
- val pFastq1a = makeFastqRecords(
- ("r01/1", "A", "", "H"),
- ("r02/1", "T", "", "H"),
- ("r03/1", "G", "", "H"),
- ("r04/1", "C", "", "H"),
- ("r05/1", "AT", "", "HH")
- )
-
- val pFastq1b = makeFastqRecords(
- ("r01/2", "A", "", "H"),
- ("r02/2", "T", "", "H"),
- ("r03/2", "G", "", "H"),
- ("r04/2", "C", "", "H"),
- ("r05/2", "AT", "", "HH")
- )
+ private def makeFeature(chr: String, start: Int, end: Int): Feature =
+ new BasicFeature(chr, start ,end)
+
+ private def makeRecord(header: String): FastqRecord =
+ new FastqRecord(header, "ATGC", "", "HIHI")
+
+ private def makeSingleRecords(headers: String*): Map[String, FastqPair] =
+ headers.map(x => (x, (makeRecord(x), null))).toMap
+
+ private def makePairRecords(headers: (String, (String, String))*): Map[String, FastqPair] =
+ headers.map(x => (x._1, (makeRecord(x._2._1), makeRecord(x._2._2)))).toMap
+
+ private def makeClue(tName: String, f: File, rName: String): String =
+ tName + " on " + f.getName + ", read " + rName + ": "
@Test def testIntervalStartEnd() = {
val obs = makeFeatureFromString(List("chr5:1000-1100")).next()
@@ -90,40 +72,74 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with Matchers {
makeFeatureFromString(List("chr5:1000-")).next()
}
- @Test def testMembershipSingleBamDefault() = {
- val feats = makeFeatures(
- ("chrQ", 30, 49), // no overlap, adjacent left of read r02
- ("chrQ", 200, 210), // no overlap, adjacent right of read r01
- ("chrQ", 220, 230), // no overlap
- ("chrQ", 430, 460), // overlap, partial on interval and read r04
- ("chrQ", 693, 698)) // overlap, interval enveloped read r03
- val memFunc = makeMembershipFunction(feats, sBam01)
- // r01 is not in the set
- memFunc(sFastq1(0), null) shouldBe false
- // r02 is not in the set
- memFunc(sFastq1(1), null) shouldBe false
- // r03 is in the set
- memFunc(sFastq1(2), null) shouldBe true
- // r04 is in the set
- memFunc(sFastq1(3), null) shouldBe true
- // r05 is not in the set
- memFunc(sFastq1(4), null) shouldBe false
+ @DataProvider(name = "singleAlnProvider1", parallel = true)
+ def singleAlnProvider1() = {
+ val sFastq1 = makeSingleRecords("r01", "r02", "r03", "r04", "r05")
+ val sFastq1Default = sFastq1.keys.map(x => (x, false)).toMap
+ val sBam01 = resourceFile("/single01.bam")
+
+ Array(
+ Array("adjacent left",
+ makeFeature("chrQ", 30, 49), sBam01, sFastq1, sFastq1Default),
+ Array("adjacent right",
+ makeFeature("chrQ", 200, 210), sBam01, sFastq1, sFastq1Default),
+ Array("no overlap",
+ makeFeature("chrQ", 220, 230), sBam01, sFastq1, sFastq1Default),
+ Array("partial overlap",
+ makeFeature("chrQ", 430, 460), sBam01, sFastq1, sFastq1Default.updated("r04", true)),
+ Array("enveloped",
+ makeFeature("chrQ", 693, 698), sBam01, sFastq1, sFastq1Default.updated("r03", true))
+ )
}
- @Test def testMembershipPairBamDefault() = {
- val feats = makeFeatures(
- ("chrQ", 30, 49), // no overlap, adjacent left of read r02
- ("chrQ", 200, 210), // no overlap, adjacent right of read r01
- ("chrQ", 220, 230), // no overlap, middle of read r01
- ("chrQ", 430, 460), // overlap, partial on interval and read r04
- ("chrQ", 693, 698), // overlap, interval enveloped read r03
- ("chrQ", 900, 999)) // enveloped inside read r05 split
- val memFunc = makeMembershipFunction(feats, pBam01, 2)
- memFunc(pFastq1a(0), pFastq1b(0)) shouldBe false
- memFunc(pFastq1a(1), pFastq1b(1)) shouldBe false
- memFunc(pFastq1a(2), pFastq1b(2)) shouldBe true
- memFunc(pFastq1a(3), pFastq1b(3)) shouldBe true
- memFunc(pFastq1a(4), pFastq1b(4)) shouldBe true
+ @Test(dataProvider = "singleAlnProvider1")
+ def testSingleBamDefault(name: String, feat: Feature, inAln: File,
+ fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+ require(resultMap.keySet == fastqMap.keySet)
+ val memFunc = makeMembershipFunction(Iterable(feat), inAln)
+ for ((key, (rec1, rec2)) <- fastqMap) {
+ withClue(makeClue(name, inAln, key)) {
+ memFunc(rec1, rec2) shouldBe resultMap(key)
+ }
+ }
}
-}
+ @DataProvider(name = "pairAlnProvider1", parallel = true)
+ def pairAlnProvider1() = {
+ val pFastq1 = makePairRecords(
+ ("r01", ("r01/1", "r01/2")),
+ ("r02", ("r02/1", "r02/2")),
+ ("r03", ("r03/1", "r03/2")),
+ ("r04", ("r04/1", "r04/2")),
+ ("r05", ("r05/1", "r05/2")))
+ val pFastq1Default = pFastq1.keys.map(x => (x, false)).toMap
+ val pBam01 = resourceFile("/paired01.bam")
+
+ Array(
+ Array("adjacent left",
+ makeFeature("chrQ", 30, 49), pBam01, pFastq1, pFastq1Default),
+ Array("adjacent right",
+ makeFeature("chrQ", 200, 210), pBam01, pFastq1, pFastq1Default),
+ Array("no overlap",
+ makeFeature("chrQ", 220, 230), pBam01, pFastq1, pFastq1Default),
+ Array("partial overlap",
+ makeFeature("chrQ", 430, 460), pBam01, pFastq1, pFastq1Default.updated("r04", true)),
+ Array("enveloped",
+ makeFeature("chrQ", 693, 698), pBam01, pFastq1, pFastq1Default.updated("r03", true)),
+ Array("in intron",
+ makeFeature("chrQ", 900, 999), pBam01, pFastq1, pFastq1Default.updated("r05", true))
+ )
+ }
+
+ @Test(dataProvider = "pairAlnProvider1")
+ def testPairBamDefault(name: String, feat: Feature, inAln: File,
+ fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+ require(resultMap.keySet == fastqMap.keySet)
+ val memFunc = makeMembershipFunction(Iterable(feat), inAln, commonSuffixLength = 2)
+ for ((key, (rec1, rec2)) <- fastqMap) {
+ withClue(makeClue(name, inAln, key)) {
+ memFunc(rec1, rec2) shouldBe resultMap(key)
+ }
+ }
+ }
+}
--
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