From 9c9edf13243970e1d98214551dc134e9c5b5984b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 10 Sep 2015 12:55:53 +0200
Subject: [PATCH] Adding -o option to hide output from stdout
---
.../sasc/biopet/tools/FindRepeatsPacBio.scala | 26 +++++++++++++++----
.../biopet/tools/FindRepeatsPacBioTest.scala | 3 ++-
2 files changed, 23 insertions(+), 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
index e6ffb81df..b6666fcf1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.tools
-import java.io.File
+import java.io.{ PrintWriter, File }
import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReaderFactory, ValidationStringency }
import nl.lumc.sasc.biopet.core.ToolCommand
@@ -24,12 +24,17 @@ import scala.collection.JavaConversions._
import scala.io.Source
object FindRepeatsPacBio extends ToolCommand {
- case class Args(inputBam: File = null, inputBed: File = null) extends AbstractArgs
+ case class Args(inputBam: File = null,
+ outputFile: Option[File] = None,
+ inputBed: File = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputBam") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputBam = x)
} text "Path to input file"
+ opt[File]('o', "outputFile") maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ } text "Path to input file"
opt[File]('b', "inputBed") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputBed = x)
} text "Path to bed file"
@@ -50,7 +55,6 @@ object FindRepeatsPacBio extends ToolCommand {
val header = List("chr", "startPos", "stopPos", "Repeat_seq", "repeatLength",
"original_Repeat_readLength", "Calculated_repeat_readLength",
"minLength", "maxLength", "inserts", "deletions", "notSpan")
- println(header.mkString("\t"))
for (
bedLine <- Source.fromFile(commandArgs.inputBed).getLines();
@@ -84,9 +88,21 @@ object FindRepeatsPacBio extends ToolCommand {
if (length < minLength || minLength == -1) minLength = length
}
}
- println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
- maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
bamIter.close()
+ commandArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(header.mkString("\t"))
+ writer.println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
+ maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
+ writer.close()
+ }
+ case _ => {
+ println(header.mkString("\t"))
+ println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
+ maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
+ }
+ }
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
index 8057c9d25..b6de2f8bc 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -28,7 +28,8 @@ class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers
@Test
def testMain() = {
- val args = Array("-I", bam, "-b", bed)
+ val outputFile = File.createTempFile("repeats", ".tsv")
+ val args = Array("-I", bam, "-b", bed, "-o", outputFile.toString)
main(args)
}
--
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