From 879c66bb715c05c9bcb3452230e3e6fc291e76be Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 30 Oct 2014 12:12:15 +0100
Subject: [PATCH] Use mocks to avoid writing to disk when testing
---
.../nl/lumc/sasc/biopet/tools/WipeReads.scala | 55 ++++++-------
.../sasc/biopet/tools/WipeReadsUnitTest.scala | 81 ++++++++-----------
2 files changed, 59 insertions(+), 77 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index 19054821b..a6c82c3b1 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -13,6 +13,7 @@ import htsjdk.samtools.SamReader
import htsjdk.samtools.SamReaderFactory
import htsjdk.samtools.QueryInterval
import htsjdk.samtools.ValidationStringency
+import htsjdk.samtools.SAMFileWriter
import htsjdk.samtools.SAMFileWriterFactory
import htsjdk.samtools.SAMRecord
import htsjdk.samtools.util.{ Interval, IntervalTreeMap }
@@ -51,7 +52,7 @@ object WipeReads extends ToolCommand {
* @param inBam input BAM file
* @return
*/
- private def prepBam(inBam: File): SamReader = {
+ private def prepInBam(inBam: File): SamReader = {
val bam = SamReaderFactory
.make()
.validationStringency(ValidationStringency.LENIENT)
@@ -60,6 +61,13 @@ object WipeReads extends ToolCommand {
bam
}
+ private def prepOutBam(outBam: File, templateBam: File,
+ writeIndex: Boolean = true, async: Boolean = true): SAMFileWriter =
+ new SAMFileWriterFactory()
+ .setCreateIndex(writeIndex)
+ .setUseAsyncIo(async)
+ .makeBAMWriter(prepInBam(templateBam).getFileHeader, true, outBam)
+
/**
* Creates a list of intervals given an input File
*
@@ -208,7 +216,7 @@ object WipeReads extends ToolCommand {
else
(r: SAMRecord) => readGroupIds.contains(r.getReadGroup.getReadGroupId)
- val readyBam = prepBam(inBam)
+ val readyBam = prepInBam(inBam)
val queryIntervals = ivl
.flatMap(x => makeQueryInterval(readyBam, x))
@@ -261,44 +269,29 @@ object WipeReads extends ToolCommand {
* @param filterFunc filter function that evaluates true for excluded SAMRecord
* @param inBam input BAM file
* @param outBam output BAM file
- * @param writeIndex whether to write index for output BAM file
- * @param async whether to write asynchronously
* @param filteredOutBam whether to write excluded SAMRecords to their own BAM file
*/
- def writeFilteredBam(filterFunc: (SAMRecord => Boolean), inBam: File, outBam: File,
- writeIndex: Boolean = true, async: Boolean = true,
- filteredOutBam: Option[File] = None) = {
-
- val factory = new SAMFileWriterFactory()
- .setCreateIndex(writeIndex)
- .setUseAsyncIo(async)
-
- val templateBam = prepBam(inBam)
- val targetBam = factory.makeBAMWriter(templateBam.getFileHeader, true, outBam)
- val filteredBam = filteredOutBam
- .map(x => factory.makeBAMWriter(templateBam.getFileHeader, true, x))
+ def writeFilteredBam(filterFunc: (SAMRecord => Boolean), inBam: SamReader, outBam: SAMFileWriter,
+ filteredOutBam: Option[SAMFileWriter] = None) = {
logger.info("Writing output file(s) ...")
try {
var (incl, excl) = (0, 0)
- for (rec <- templateBam.asScala) {
+ for (rec <- inBam.asScala) {
if (!filterFunc(rec)) {
- targetBam.addAlignment(rec)
+ outBam.addAlignment(rec)
incl += 1
} else {
excl += 1
- filteredBam match {
- case None =>
- case Some(x) => x.addAlignment(rec)
- }
+ filteredOutBam.foreach(x => x.addAlignment(rec))
}
}
- println(List("input_bam", "output_bam", "count_included", "count_excluded").mkString("\t"))
- println(List(inBam.getName, outBam.getName, incl, excl).mkString("\t"))
+ println(List("count_included", "count_excluded").mkString("\t"))
+ println(List(incl, excl).mkString("\t"))
} finally {
- templateBam.close()
- targetBam.close()
- filteredBam.foreach(x => x.close())
+ inBam.close()
+ outBam.close()
+ filteredOutBam.foreach(x => x.close())
}
}
@@ -391,6 +384,7 @@ object WipeReads extends ToolCommand {
val commandArgs: Args = parseArgs(args)
+ // cannot use SamReader as inBam directly since it only allows one active iterator at any given time
val filterFunc = makeFilterNotFunction(
ivl = makeIntervalFromFile(commandArgs.targetRegions),
inBam = commandArgs.inputBam,
@@ -403,10 +397,9 @@ object WipeReads extends ToolCommand {
writeFilteredBam(
filterFunc,
- commandArgs.inputBam,
- commandArgs.outputBam,
- writeIndex = !commandArgs.noMakeIndex,
- filteredOutBam = commandArgs.filteredOutBam
+ prepInBam(commandArgs.inputBam),
+ prepOutBam(commandArgs.outputBam, commandArgs.inputBam, writeIndex = !commandArgs.noMakeIndex),
+ commandArgs.filteredOutBam.map(x => prepOutBam(x, commandArgs.inputBam, writeIndex = !commandArgs.noMakeIndex))
)
}
}
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
index 15ec3a3c4..772ed6295 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
+++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
@@ -9,6 +9,7 @@ import java.nio.file.Paths
import scala.collection.JavaConverters._
import htsjdk.samtools.SAMFileHeader
+import htsjdk.samtools.SAMFileWriter
import htsjdk.samtools.SAMLineParser
import htsjdk.samtools.SAMReadGroupRecord
import htsjdk.samtools.SAMRecord
@@ -18,10 +19,13 @@ import htsjdk.samtools.SamReaderFactory
import htsjdk.samtools.ValidationStringency
import htsjdk.samtools.util.Interval
import org.scalatest.Matchers
+import org.mockito.Matchers._
+import org.mockito.Mockito.{ inOrder => inOrd, times, verify }
+import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
-class WipeReadsUnitTest extends TestNGSuite with Matchers {
+class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
import WipeReads._
@@ -371,82 +375,67 @@ class WipeReadsUnitTest extends TestNGSuite with Matchers {
filterNotFunc(pBamRecs2(8)) shouldBe false
filterNotFunc(pBamRecs2(9)) shouldBe false
}
-
@Test def testWriteSingleBamDefault() = {
val mockFilterOutFunc = (r: SAMRecord) => Set("r03", "r04", "r05").contains(r.getReadName)
- val outBam = makeTempBam()
- val outBamIndex = makeTempBamIndex(outBam)
- outBam.deleteOnExit()
- outBamIndex.deleteOnExit()
+ val outBam = mock[SAMFileWriter]
val stdout = new java.io.ByteArrayOutputStream
Console.withOut(stdout) {
- writeFilteredBam(mockFilterOutFunc, sBamFile1, outBam)
+ writeFilteredBam(mockFilterOutFunc, makeSamReader(sBamFile1), outBam)
}
stdout.toString should ===(
- "input_bam\toutput_bam\tcount_included\tcount_excluded\n%s\t%s\t%d\t%d\n"
- .format(sBamFile1.getName, outBam.getName, 4, 3)
+ "count_included\tcount_excluded\n%d\t%d\n"
+ .format(4, 3)
)
- val exp = makeSamReader(sBamFile3).asScala
- val obs = makeSamReader(outBam).asScala
- for ((e, o) <- exp.zip(obs))
- e.getSAMString should ===(o.getSAMString)
- outBam should be('exists)
- outBamIndex should be('exists)
+ val exp = makeSamReader(sBamFile3).asScala.toList
+ verify(outBam, times(4)).addAlignment(anyObject.asInstanceOf[SAMRecord])
+ val obs = inOrd(outBam)
+ exp.foreach(x => {
+ obs.verify(outBam).addAlignment(x)
+ })
}
@Test def testWriteSingleBamAndFilteredBAM() = {
val mockFilterOutFunc = (r: SAMRecord) => Set("r03", "r04", "r05").contains(r.getReadName)
- val outBam = makeTempBam()
- val outBamIndex = makeTempBamIndex(outBam)
- outBam.deleteOnExit()
- outBamIndex.deleteOnExit()
- val filteredOutBam = makeTempBam()
- val filteredOutBamIndex = makeTempBamIndex(filteredOutBam)
- filteredOutBam.deleteOnExit()
- filteredOutBamIndex.deleteOnExit()
+ val outBam = mock[SAMFileWriter]
+ val filtBam = Some(mock[SAMFileWriter])
val stdout = new java.io.ByteArrayOutputStream
Console.withOut(stdout) {
- writeFilteredBam(mockFilterOutFunc, sBamFile1, outBam, filteredOutBam = Some(filteredOutBam))
+ writeFilteredBam(mockFilterOutFunc, makeSamReader(sBamFile1), outBam, filteredOutBam = filtBam)
}
stdout.toString should ===(
- "input_bam\toutput_bam\tcount_included\tcount_excluded\n%s\t%s\t%d\t%d\n"
- .format(sBamFile1.getName, outBam.getName, 4, 3)
+ "count_included\tcount_excluded\n%d\t%d\n"
+ .format(4, 3)
)
val exp = makeSamReader(sBamFile4).asScala
- val obs = makeSamReader(filteredOutBam).asScala
- for ((e, o) <- exp.zip(obs))
- e.getSAMString should ===(o.getSAMString)
- outBam should be('exists)
- outBamIndex should be('exists)
- filteredOutBam should be('exists)
- filteredOutBamIndex should be('exists)
+ verify(filtBam.get, times(3)).addAlignment(anyObject.asInstanceOf[SAMRecord])
+ val obs = inOrd(filtBam.get)
+ exp.foreach(x => {
+ obs.verify(filtBam.get).addAlignment(x)
+ })
}
@Test def testWritePairBamDefault() = {
val mockFilterOutFunc = (r: SAMRecord) => Set("r03", "r04", "r05").contains(r.getReadName)
- val outBam = makeTempBam()
- val outBamIndex = makeTempBamIndex(outBam)
- outBam.deleteOnExit()
- outBamIndex.deleteOnExit()
+ val outBam = mock[SAMFileWriter]
val stdout = new java.io.ByteArrayOutputStream
Console.withOut(stdout) {
- writeFilteredBam(mockFilterOutFunc, pBamFile1, outBam)
+ writeFilteredBam(mockFilterOutFunc, makeSamReader(pBamFile1), outBam)
}
stdout.toString should ===(
- "input_bam\toutput_bam\tcount_included\tcount_excluded\n%s\t%s\t%d\t%d\n"
- .format(pBamFile1.getName, outBam.getName, 8, 6)
+ "count_included\tcount_excluded\n%d\t%d\n"
+ .format(8, 6)
)
- val exp = makeSamReader(pBamFile3).asScala
- val obs = makeSamReader(outBam).asScala
- for ((e, o) <- exp.zip(obs))
- e.getSAMString should ===(o.getSAMString)
- outBam should be('exists)
- outBamIndex should be('exists)
+ val exp = makeSamReader(pBamFile3).asScala.toList
+ verify(outBam, times(8)).addAlignment(anyObject.asInstanceOf[SAMRecord])
+ val obs = inOrd(outBam)
+ exp.foreach(x => {
+ obs.verify(outBam).addAlignment(x)
+ })
}
@Test def testArgsMinimum() = {
--
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