From 162f02edbb6e7b8eb382f049d598c46a92afb381 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 1 Feb 2016 14:33:53 +0100
Subject: [PATCH] Added test on main method
---
.../lumc/sasc/biopet/tools/BaseCounter.scala | 42 +++++++++---------
.../src/test/resources/chrQ.refflat | 1 +
.../biopet-tools/src/test/resources/empty.bai | Bin 0 -> 104 bytes
.../biopet-tools/src/test/resources/empty.bam | Bin 0 -> 189 bytes
.../sasc/biopet/tools/BaseCounterTest.scala | 20 +++++++++
5 files changed, 43 insertions(+), 20 deletions(-)
create mode 100644 public/biopet-tools/src/test/resources/chrQ.refflat
create mode 100644 public/biopet-tools/src/test/resources/empty.bai
create mode 100644 public/biopet-tools/src/test/resources/empty.bam
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 756e187a6..7a2b0907f 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -56,7 +56,7 @@ object BaseCounter extends ToolCommand {
val overlapGenes = groupGenesOnOverlap(geneReader.getAll)
logger.info("Start reading bamFile")
- val counts = (for (genes <- overlapGenes.values.flatten.par) yield bamToGeneCount(cmdArgs.bamFile, genes)).toList
+ val counts = (for (genes <- overlapGenes.values.flatten.par) yield runThread(cmdArgs.bamFile, genes)).toList
logger.info("Done reading bamFile")
writeGeneCounts(counts.flatMap(_.geneCounts), cmdArgs.outputDir, cmdArgs.prefix)
@@ -281,7 +281,7 @@ object BaseCounter extends ToolCommand {
nonStrandedMetaExonCounts: List[(String, RegionCount)],
strandedMetaExonCounts: List[(String, RegionCount)])
- def bamToGeneCount(bamFile: File, genes: List[Gene]): ThreadOutput = {
+ private[tools] def runThread(bamFile: File, genes: List[Gene]): ThreadOutput = {
val counts = genes.map(gene => gene -> new GeneCount(gene)).toMap
val bamReader = SamReaderFactory.makeDefault().open(bamFile)
@@ -304,25 +304,27 @@ object BaseCounter extends ToolCommand {
}
def createMetaExonCounts(genes: List[Gene]): List[(String, RegionCount)] = {
- val regions = genes.map(gene => gene.getName -> generateMergedExonRegions(gene).sorted)
- val chr = genes.head.getContig
- val begin = regions.map(_._2.allRecords.head.start).min
- val end = regions.map(_._2.allRecords.last.end).max
-
- val posibleEnds = (regions.flatMap(_._2.allRecords.map(_.end)) ++ regions.flatMap(_._2.allRecords.map(_.start))).distinct.sorted
-
- def mergeRegions(newBegin: Int, output: List[(String, RegionCount)] = Nil): List[(String, RegionCount)] = {
- val newEnds = posibleEnds.filter(_ > newBegin)
- if (newBegin > end || newEnds.isEmpty) output
- else {
- val newEnd = newEnds.min
- val record = BedRecord(chr, newBegin, newEnd)
- val names = regions.filter(_._2.overlapWith(record).nonEmpty).map(_._1)
- if (names.nonEmpty) mergeRegions(newEnd, (names.mkString(","), new RegionCount(record.start + 1, record.end)) :: output)
- else mergeRegions(newEnd, output)
+ if (genes.nonEmpty) {
+ val regions = genes.map(gene => gene.getName -> generateMergedExonRegions(gene).sorted)
+ val chr = genes.head.getContig
+ val begin = regions.map(_._2.allRecords.head.start).min
+ val end = regions.map(_._2.allRecords.last.end).max
+
+ val posibleEnds = (regions.flatMap(_._2.allRecords.map(_.end)) ++ regions.flatMap(_._2.allRecords.map(_.start))).distinct.sorted
+
+ def mergeRegions(newBegin: Int, output: List[(String, RegionCount)] = Nil): List[(String, RegionCount)] = {
+ val newEnds = posibleEnds.filter(_ > newBegin)
+ if (newBegin > end || newEnds.isEmpty) output
+ else {
+ val newEnd = newEnds.min
+ val record = BedRecord(chr, newBegin, newEnd)
+ val names = regions.filter(_._2.overlapWith(record).nonEmpty).map(_._1)
+ if (names.nonEmpty) mergeRegions(newEnd, (names.mkString(","), new RegionCount(record.start + 1, record.end)) :: output)
+ else mergeRegions(newEnd, output)
+ }
}
- }
- mergeRegions(begin)
+ mergeRegions(begin)
+ } else Nil
}
def bamRecordBasesOverlap(samRecord: SAMRecord, start: Int, end: Int): Int = {
diff --git a/public/biopet-tools/src/test/resources/chrQ.refflat b/public/biopet-tools/src/test/resources/chrQ.refflat
new file mode 100644
index 000000000..dfcc51100
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/chrQ.refflat
@@ -0,0 +1 @@
+geneA t1 chrQ + 200 500 225 475 3 200,300,400 250,350,500
diff --git a/public/biopet-tools/src/test/resources/empty.bai b/public/biopet-tools/src/test/resources/empty.bai
new file mode 100644
index 0000000000000000000000000000000000000000..e4e22396b4877369154096123eaf25e8bb47503a
GIT binary patch
literal 104
ucmZ>A^kigWU|;}YPay^dMj%}S#2~N_LNRzvg2<zbgVZ7eWWC7ZAT|JCaRmMV
literal 0
HcmV?d00001
diff --git a/public/biopet-tools/src/test/resources/empty.bam b/public/biopet-tools/src/test/resources/empty.bam
new file mode 100644
index 0000000000000000000000000000000000000000..bd4073d80cbf73c689e97d2814f9b1fd00d63895
GIT binary patch
literal 189
zcmb2|=3rp}f&Xj_PR>jW3mA%vzNGRbCnOYnD0s;8d9%?K<EK2|wtJmBukUs8jJJ;G
z(;^POCp_Oad!5tZdh&%)%YcDN<)8u(mHYXNYcn%DpG$~eJ?Y9LAw9JPC)YUeTso_;
zfbTg=qh%S7K!IRKWR6X%M5Bqg!2fop2{98J1rIYR++D%cq_t{QR@SRmQc{lZ0v)O)
X7(`S2e(eLgOCHUE(hSUC_ksujDyu*2
literal 0
HcmV?d00001
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
index 2ec0b6080..09a7fde18 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BaseCounterTest.scala
@@ -1,5 +1,9 @@
package nl.lumc.sasc.biopet.tools
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
import htsjdk.samtools.{SAMReadGroupRecord, SAMSequenceRecord, SAMLineParser, SAMFileHeader}
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
@@ -164,6 +168,22 @@ class BaseCounterTest extends TestNGSuite with Matchers {
assert(ab.exists(x => x._1 == "geneB" && x._2.start == 201 && x._2.end == 210))
assert(ab.exists(x => x._1 == "geneB" && x._2.start == 221 && x._2.end == 250))
}
+
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testMain: Unit = {
+ val outputDir = Files.createTempDir()
+ outputDir.deleteOnExit()
+ val prefix = "test"
+ val bamFile = new File(resourcePath("/empty.bam"))
+ val refflat = new File(resourcePath("/chrQ.refflat"))
+ main(Array("-o", outputDir.getAbsolutePath, "-p", prefix,
+ "-b", bamFile.getAbsolutePath, "-r", refflat.getAbsolutePath))
+ outputDir.list().size shouldBe 34
+ }
}
object BaseCounterTest {
--
GitLab