diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
index dc1d98156e2a67122d6ef299df742549faafb1af..72dbf81c95336340483620d1e515cde61c1cd128 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
@@ -15,6 +15,9 @@
*/
package nl.lumc.sasc.biopet.tools
+import java.text.DecimalFormat
+import java.util
+
import htsjdk.variant.vcf.VCFFileReader
import java.io.File
import java.io.PrintStream
@@ -28,8 +31,9 @@ class VcfToTsv {
object VcfToTsv extends ToolCommand {
case class Args(inputFile: File = null, outputFile: File = null, fields: List[String] = Nil, infoFields: List[String] = Nil,
- sampleFileds: List[String] = Nil, disableDefaults: Boolean = false,
- allInfo: Boolean = false, allFormat: Boolean = false) extends AbstractArgs
+ sampleFields: List[String] = Nil, disableDefaults: Boolean = false,
+ allInfo: Boolean = false, allFormat: Boolean = false,
+ separator: String = "\t", listSeparator: String = ",", maxDecimals: Int = 2) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
@@ -51,19 +55,35 @@ object VcfToTsv extends ToolCommand {
c.copy(allFormat = true)
}
opt[String]('s', "sample_field") unbounded () action { (x, c) =>
- c.copy(sampleFileds = x :: c.sampleFileds)
+ c.copy(sampleFields = x :: c.sampleFields)
}
opt[Unit]('d', "disable_defaults") unbounded () action { (x, c) =>
c.copy(disableDefaults = true)
}
+ opt[String]("separator") maxOccurs (1) action { (x, c) =>
+ c.copy(separator = x)
+ } text ("Optional separator. Default is tab-delimited")
+ opt[String]("list_separator") maxOccurs (1) action { (x, c) =>
+ c.copy(listSeparator = x)
+ } text ("Optional list separator. By default, lists are separated by a comma")
+ opt[Int]("max_decimals") maxOccurs(1) action { (x, c) =>
+ c.copy(maxDecimals = x)
+ } text ("Number of decimal places for numbers. Default is 2")
}
- val defaultFields = List("chr", "pos", "id", "ref", "alt", "qual")
+ val defaultFields = List("CHROM", "POS", "ID", "REF", "ALT", "QUAL")
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+ // Throw exception if separator and listSeparator are identical
+ if (commandArgs.separator == commandArgs.listSeparator) throw new IllegalArgumentException(
+ "Separator and list_separator should not be identical"
+ )
+
+ val formatter = createFormatter(commandArgs.maxDecimals)
+
val reader = new VCFFileReader(commandArgs.inputFile, false)
val header = reader.getFileHeader
val samples = header.getSampleNamesInOrder
@@ -75,49 +95,37 @@ object VcfToTsv extends ToolCommand {
commandArgs.fields.toSet[String] ++
(if (commandArgs.allInfo) allInfoFields else commandArgs.infoFields).map("INFO-" + _) ++ {
val buffer: ListBuffer[String] = ListBuffer()
- for (f <- (if (commandArgs.allFormat) allFormatFields else commandArgs.sampleFileds); sample <- samples) {
+ for (f <- (if (commandArgs.allFormat) allFormatFields else commandArgs.sampleFields); sample <- samples) {
buffer += sample + "-" + f
}
buffer.toSet[String]
}
- val sortedFields = fields.toList.sortWith((a, b) => {
- val aT = if (a.startsWith("INFO-")) 'i' else if (samples.exists(x => a.startsWith(x + "-"))) 'f' else 'g'
- val bT = if (b.startsWith("INFO-")) 'i' else if (samples.exists(x => b.startsWith(x + "-"))) 'f' else 'g'
- if (aT == 'g' && bT == 'g') {
- val ai = defaultFields.indexOf(a)
- val bi = defaultFields.indexOf(b)
- if (bi < 0) true
- else ai <= bi
- } else if (aT == 'g') true
- else if (bT == 'g') false
- else if (aT == bT) (if (a.compareTo(b) > 0) false else true)
- else if (aT == 'i') true
- else false
- })
- val witter = if (commandArgs.outputFile != null) new PrintStream(commandArgs.outputFile)
+ val sortedFields = sortFields(fields, samples.toList)
+
+ val writer = if (commandArgs.outputFile != null) new PrintStream(commandArgs.outputFile)
else sys.process.stdout
- witter.println(sortedFields.mkString("#", "\t", ""))
+ writer.println(sortedFields.mkString("#", commandArgs.separator, ""))
for (vcfRecord <- reader) {
val values: Map[String, Any] = Map()
- values += "chr" -> vcfRecord.getChr
- values += "pos" -> vcfRecord.getStart
- values += "id" -> vcfRecord.getID
- values += "ref" -> vcfRecord.getReference.getBaseString
- values += "alt" -> {
+ values += "CHROM" -> vcfRecord.getChr
+ values += "POS" -> vcfRecord.getStart
+ values += "ID" -> vcfRecord.getID
+ values += "REF" -> vcfRecord.getReference.getBaseString
+ values += "ALT" -> {
val t = for (a <- vcfRecord.getAlternateAlleles) yield a.getBaseString
- t.mkString(",")
+ t.mkString(commandArgs.listSeparator)
}
- values += "qual" -> (if (vcfRecord.getPhredScaledQual == -10) "." else scala.math.round(vcfRecord.getPhredScaledQual * 100.0) / 100.0)
- values += "filter" -> vcfRecord.getFilters
+ values += "QUAL" -> (if (vcfRecord.getPhredScaledQual == -10) "." else formatter.format(vcfRecord.getPhredScaledQual))
+ values += "INFO" -> vcfRecord.getFilters
for ((field, content) <- vcfRecord.getAttributes) {
values += "INFO-" + field -> {
content match {
- case a: List[_] => a.mkString(",")
- case a: Array[_] => a.mkString(",")
- case a: java.util.ArrayList[_] => a.mkString(",")
+ case a: List[_] => a.mkString(commandArgs.listSeparator)
+ case a: Array[_] => a.mkString(commandArgs.listSeparator)
+ case a: java.util.ArrayList[_] => a.mkString(commandArgs.listSeparator)
case _ => content
}
}
@@ -129,10 +137,10 @@ object VcfToTsv extends ToolCommand {
val l = for (g <- genotype.getAlleles) yield vcfRecord.getAlleleIndex(g)
l.map(x => if (x < 0) "." else x).mkString("/")
}
- if (genotype.hasAD) values += sample + "-AD" -> List(genotype.getAD: _*).mkString(",")
- if (genotype.hasDP) values += sample + "-DP" -> genotype.getDP
- if (genotype.hasGQ) values += sample + "-GQ" -> genotype.getGQ
- if (genotype.hasPL) values += sample + "-PL" -> List(genotype.getPL: _*).mkString(",")
+ if (genotype.hasAD) values += sample + "-AD" -> List(genotype.getAD: _*).mkString(commandArgs.listSeparator)
+ if (genotype.hasDP) values += sample + "-DP" -> genotype.getDP
+ if (genotype.hasGQ) values += sample + "-GQ" -> genotype.getGQ
+ if (genotype.hasPL) values += sample + "-PL" -> List(genotype.getPL: _*).mkString(commandArgs.listSeparator)
for ((field, content) <- genotype.getExtendedAttributes) {
values += sample + "-" + field -> content
}
@@ -142,7 +150,58 @@ object VcfToTsv extends ToolCommand {
values(f)
} else ""
}
- witter.println(line.mkString("\t"))
+ writer.println(line.mkString(commandArgs.separator))
}
}
+
+ /**
+ * This function creates a correct DecimalFormat for a specific length of decimals
+ * @param len number of decimal places
+ * @return DecimalFormat formatter
+ */
+ def createFormatter(len: Int): DecimalFormat = {
+ val patternString = "###." + (for (x <- (1 to len)) yield "#").mkString("")
+ new DecimalFormat(patternString)
+ }
+
+
+ /**
+ * This fields sorts fields, such that non-info and non-sample specific fields (e.g. general ones) are on front
+ * followed by info fields
+ * followed by sample-specific fields
+ * @param fields fields
+ * @param samples samples
+ * @return sorted samples
+ */
+ def sortFields(fields: Set[String], samples: List[String]): List[String] = {
+ def fieldType(x: String) = x match {
+ case _ if x.startsWith("INFO-") => 'i'
+ case _ if (samples.exists(y => x.startsWith(y + "-"))) => 'f'
+ case _ => 'g'
+ }
+
+ fields.toList.sortWith((a, b) => {
+ (fieldType(a), fieldType(b)) match {
+ case ('g','g') => {
+ val ai = defaultFields.indexOf(a)
+ val bi = defaultFields.indexOf(b)
+ if (bi < 0) true else ai <= bi
+ }
+ case ('f', 'f') => {
+ val sampleA = a.split("-").head
+ val sampleB = b.split("-").head
+ sampleA.compareTo(sampleB) match {
+ case 0 => !(a.compareTo(b) > 0)
+ case i if (i > 0) => false
+ case _ => true
+ }
+ }
+ case ('g', _) => true
+ case (_, 'g') => false
+ case (a, b) if a == b => !(a.compareTo(b) > 0)
+ case ('i', _) => true
+ case _ => false
+ }
+ })
+ }
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..598f4550d3f9743ae63f6ca3196c236b39b774d9
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
@@ -0,0 +1,70 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.nio.file.Paths
+import java.util
+import scala.collection.JavaConversions._
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Random
+
+/**
+ * Created by ahbbollen on 13-4-15.
+ */
+class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
+ import VcfToTsv._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val rand = new Random()
+
+ val vepped = resourcePath("/VEP_oneline.vcf")
+ val unvepped = resourcePath("/unvepped.vcf")
+
+ @Test def testAllFields() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", unvepped, "-o", tmp_path, "--all_info")
+ main(arguments)
+ }
+
+ @Test def testSpecificField() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "-i", "CSQ")
+ main(arguments)
+ }
+
+ @Test def testNewSeparators() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",", "--list_separator", "|")
+ main(arguments)
+ }
+
+ @Test(expectedExceptions = Array(classOf[IllegalArgumentException]))
+ def testIdenticalSeparators() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",")
+ main(arguments)
+ }
+
+ @Test def testFormatter() = {
+ val formatter = createFormatter(2)
+ formatter.format(5000.12345) should be("5000.12")
+ val nformatter = createFormatter(3)
+ nformatter.format(5000.12345) should be("5000.123")
+ }
+
+ @Test def testSortFields() = {
+ val unsortedFields = Set("Child01-GT", "Mother02-GT", "Father03-GT", "INFO-Something", "INFO-ScoreSomething",
+ "INFO-AlleleScoreSomething", "WeirdField")
+ val samples = List("Child01", "Father03", "Mother02")
+
+ val sorted = sortFields(unsortedFields, samples)
+ sorted should be(List("WeirdField", "INFO-AlleleScoreSomething", "INFO-ScoreSomething", "INFO-Something",
+ "Child01-GT", "Father03-GT", "Mother02-GT"))
+ }
+
+}