From 1b93ce1c44350f98cc98c2d5dbb9e8c732356589 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 18:29:42 +0100
Subject: [PATCH] ExtractAlignedFastq fix for FASTQ records with descriptions
---
.../sasc/biopet/tools/ExtractAlignedFastq.scala | 13 +++++++++----
biopet-framework/src/test/resources/paired01a.fq | 2 +-
biopet-framework/src/test/resources/paired01b.fq | 2 +-
.../biopet/tools/ExtractAlignedFastqUnitTest.scala | 8 ++++----
4 files changed, 15 insertions(+), 10 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 7f7fe2239..8ceb27793 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
@@ -21,6 +21,9 @@ object ExtractAlignedFastq extends ToolCommand {
type FastqInput = (FastqRecord, Option[FastqRecord])
+ /** function to get FastqRecord ID */
+ def fastqId(rec: FastqRecord) = rec.getReadHeader.split(" ")(0)
+
/**
* Function to create iterator over Interval given input interval string
*
@@ -113,11 +116,12 @@ object ExtractAlignedFastq extends ToolCommand {
)
(pair: FastqInput) => pair._2 match {
- case None => selected.contains(pair._1.getReadHeader)
+ case None => selected.contains(fastqId(pair._1))
case Some(x) =>
- require(commonSuffixLength < pair._1.getReadHeader.length)
- require(commonSuffixLength < x.getReadHeader.length)
- selected.contains(pair._1.getReadHeader.dropRight(commonSuffixLength))
+ val rec1Id = fastqId(pair._1)
+ require(commonSuffixLength < rec1Id.length)
+ require(commonSuffixLength < fastqId(x).length)
+ selected.contains(rec1Id.dropRight(commonSuffixLength))
}
}
@@ -224,6 +228,7 @@ object ExtractAlignedFastq extends ToolCommand {
minMapQ = commandArgs.minMapQ,
commonSuffixLength = commandArgs.commonSuffixLength)
+ logger.info("Writing to output file(s) ...")
(commandArgs.inputFastq2, commandArgs.outputFastq2) match {
case (None, None) => extractReads(memFunc,
diff --git a/biopet-framework/src/test/resources/paired01a.fq b/biopet-framework/src/test/resources/paired01a.fq
index 530a1bb9b..d1fcedf37 100644
--- a/biopet-framework/src/test/resources/paired01a.fq
+++ b/biopet-framework/src/test/resources/paired01a.fq
@@ -1,4 +1,4 @@
-@r01/1
+@r01/1 hello
A
+
H
diff --git a/biopet-framework/src/test/resources/paired01b.fq b/biopet-framework/src/test/resources/paired01b.fq
index 72cf9246d..b93021532 100644
--- a/biopet-framework/src/test/resources/paired01b.fq
+++ b/biopet-framework/src/test/resources/paired01b.fq
@@ -1,4 +1,4 @@
-@r01/2
+@r01/2 hello
T
+
I
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 4cd7205c0..e60af8466 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
@@ -189,7 +189,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
}
@Test def testWriteSingleFastqDefault() = {
- val memFunc = (recs: FastqInput) => Set("r01", "r03").contains(recs._1.getReadHeader)
+ val memFunc = (recs: FastqInput) => Set("r01", "r03").contains(fastqId(recs._1))
val in1 = new FastqReader(resourceFile("/single01.fq"))
val mo1 = mock[BasicFastqWriter]
val obs = inOrd(mo1)
@@ -201,15 +201,15 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
@Test def testWritePairFastqDefault() = {
val mockSet = Set("r01/1", "r01/2", "r03/1", "r03/2")
- val memFunc = (recs: FastqInput) => mockSet.contains(recs._1.getReadHeader) || mockSet.contains(recs._2.get.getReadHeader)
+ val memFunc = (recs: FastqInput) => mockSet.contains(fastqId(recs._1)) || mockSet.contains(fastqId(recs._2.get))
val in1 = new FastqReader(resourceFile("/paired01a.fq"))
val in2 = new FastqReader(resourceFile("/paired01b.fq"))
val mo1 = mock[BasicFastqWriter]
val mo2 = mock[BasicFastqWriter]
val obs = inOrd(mo1, mo2)
extractReads(memFunc, in1, mo1, in2, mo2)
- obs.verify(mo1).write(new FastqRecord("r01/1", "A", "", "H"))
- obs.verify(mo2).write(new FastqRecord("r01/2", "T", "", "I"))
+ obs.verify(mo1).write(new FastqRecord("r01/1 hello", "A", "", "H"))
+ obs.verify(mo2).write(new FastqRecord("r01/2 hello", "T", "", "I"))
obs.verify(mo1).write(new FastqRecord("r03/1", "G", "", "H"))
obs.verify(mo2).write(new FastqRecord("r03/2", "C", "", "I"))
verify(mo1, times(2)).write(anyObject.asInstanceOf[FastqRecord])
--
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