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biopet.biopet
Commit 2cd2e497 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added chromosome specific stats

parent 21a84095
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Showing with 100 additions and 128 deletions
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @ 2cd2e497
......@@ -102,7 +102,7 @@ object VcfStats extends ToolCommand {
* @param genotypeStats Stores all genotype relative stats
* @param sampleToSample Stores sample to sample compare stats
*/
case class SampleStats(val genotypeStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map(),
case class SampleStats(val genotypeStats: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map(),
val sampleToSample: mutable.Map[String, SampleToSampleStats] = mutable.Map()) {
/** Add an other class */
def +=(other: SampleStats): Unit = {
......@@ -110,10 +110,11 @@ object VcfStats extends ToolCommand {
if (this.sampleToSample.contains(key)) this.sampleToSample(key) += value
else this.sampleToSample(key) = value
}
for ((field, fieldMap) <- other.genotypeStats) {
val thisField = this.genotypeStats.get(field)
for ((chr, chrMap) <- other.genotypeStats; (field, fieldMap) <- chrMap) {
if (!this.genotypeStats.contains(chr)) genotypeStats += (chr -> mutable.Map[String, mutable.Map[Any, Int]]())
val thisField = this.genotypeStats(chr).get(field)
if (thisField.isDefined) mergeStatsMap(thisField.get, fieldMap)
else this.genotypeStats += field -> fieldMap
else this.genotypeStats(chr) += field -> fieldMap
}
}
}
......@@ -123,7 +124,7 @@ object VcfStats extends ToolCommand {
* @param generalStats Stores are general stats
* @param samplesStats Stores all sample/genotype specific stats
*/
case class Stats(val generalStats: mutable.Map[String, mutable.Map[Any, Int]] = mutable.Map(),
case class Stats(val generalStats: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map(),
val samplesStats: mutable.Map[String, SampleStats] = mutable.Map()) {
/** Add an other class */
def +=(other: Stats): Stats = {
......@@ -131,38 +132,34 @@ object VcfStats extends ToolCommand {
if (this.samplesStats.contains(key)) this.samplesStats(key) += value
else this.samplesStats(key) = value
}
for ((field, fieldMap) <- other.generalStats) {
val thisField = this.generalStats.get(field)
for ((chr, chrMap) <- other.generalStats; (field, fieldMap) <- chrMap) {
if (!this.generalStats.contains(chr)) generalStats += (chr -> mutable.Map[String, mutable.Map[Any, Int]]())
val thisField = this.generalStats(chr).get(field)
if (thisField.isDefined) mergeStatsMap(thisField.get, fieldMap)
else this.generalStats += field -> fieldMap
else this.generalStats(chr) += field -> fieldMap
}
this
}
}
/**
* Merge m2 into m1
* @param m1
* @param m2
*/
/** Merge m2 into m1 */
def mergeStatsMap(m1: mutable.Map[Any, Int], m2: mutable.Map[Any, Int]): Unit = {
for (key <- m2.keySet)
m1(key) = m1.getOrElse(key, 0) + m2(key)
}
/**
* Merge m2 into m1
* @param m1
* @param m2
*/
def mergeNestedStatsMap(m1: mutable.Map[String, mutable.Map[Any, Int]], m2: Map[String, Map[Any, Int]]): Unit = {
for ((field, fieldMap) <- m2) {
if (m1.contains(field)) {
for ((key, value) <- fieldMap) {
if (m1(field).contains(key)) m1(field)(key) += value
else m1(field)(key) = value
}
} else m1(field) = mutable.Map(fieldMap.toList: _*)
/** Merge m2 into m1 */
def mergeNestedStatsMap(m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]],
m2: Map[String, Map[String, Map[Any, Int]]]): Unit = {
for ((chr, chrMap) <- m2; (field, fieldMap) <- chrMap) {
if (m1.contains(chr)) {
if (m1(chr).contains(field)) {
for ((key, value) <- fieldMap) {
if (m1(chr)(field).contains(key)) m1(chr)(field)(key) += value
else m1(chr)(field)(key) = value
}
} else m1(chr)(field) = mutable.Map(fieldMap.toList: _*)
} else m1(chr) = mutable.Map(field -> mutable.Map(fieldMap.toList: _*))
}
}
......@@ -227,8 +224,8 @@ object VcfStats extends ToolCommand {
val stats = createStats
logger.info("Starting on: " + interval)
for (
record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd
for (record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd)
if record.getStart <= interval.getEnd
) {
mergeNestedStatsMap(stats.generalStats, checkGeneral(record))
for (sample1 <- samples) yield {
......@@ -251,8 +248,8 @@ object VcfStats extends ToolCommand {
logger.info("Done reading vcf records")
writeField("QUAL", stats.generalStats.getOrElse("QUAL", mutable.Map()))
writeField("general", stats.generalStats.getOrElse("general", mutable.Map()))
writeField("QUAL", stats.generalStats.getOrElse("total", mutable.Map()).getOrElse("QUAL", mutable.Map()))
writeField("general", stats.generalStats.getOrElse("total", mutable.Map()).getOrElse("general", mutable.Map()))
writeGenotypeFields(stats, commandArgs.outputDir + "/genotype_", samples)
writeOverlap(stats, _.genotypeOverlap, commandArgs.outputDir + "/sample_compare/genotype_overlap", samples)
writeOverlap(stats, _.alleleOverlap, commandArgs.outputDir + "/sample_compare/allele_overlap", samples)
......@@ -260,56 +257,49 @@ object VcfStats extends ToolCommand {
logger.info("Done")
}
/**
* Function to check all general stats, all info expect sample/genotype specific stats
* @param record
* @return
*/
protected def checkGeneral(record: VariantContext): Map[String, Map[Any, Int]] = {
/** Function to check all general stats, all info expect sample/genotype specific stats */
protected def checkGeneral(record: VariantContext): Map[String, Map[String, Map[Any, Int]]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any): Unit = {
def addToBuffer(key: String, value: Any, found:Boolean): Unit = {
val map = buffer.getOrElse(key, Map())
buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
if (found) buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
else buffer += key -> (map + (value -> (map.getOrElse(value, 0))))
}
buffer += "QUAL" -> Map(record.getPhredScaledQual -> 1)
addToBuffer("general", "Total")
if (record.isBiallelic) addToBuffer("general", "Biallelic")
if (record.isComplexIndel) addToBuffer("general", "ComplexIndel")
if (record.isFiltered) addToBuffer("general", "Filtered")
if (record.isFullyDecoded) addToBuffer("general", "FullyDecoded")
if (record.isIndel) addToBuffer("general", "Indel")
if (record.isMixed) addToBuffer("general", "Mixed")
if (record.isMNP) addToBuffer("general", "MNP")
if (record.isMonomorphicInSamples) addToBuffer("general", "MonomorphicInSamples")
if (record.isNotFiltered) addToBuffer("general", "NotFiltered")
if (record.isPointEvent) addToBuffer("general", "PointEvent")
if (record.isPolymorphicInSamples) addToBuffer("general", "PolymorphicInSamples")
if (record.isSimpleDeletion) addToBuffer("general", "SimpleDeletion")
if (record.isSimpleInsertion) addToBuffer("general", "SimpleInsertion")
if (record.isSNP) addToBuffer("general", "SNP")
if (record.isStructuralIndel) addToBuffer("general", "StructuralIndel")
if (record.isSymbolic) addToBuffer("general", "Symbolic")
if (record.isSymbolicOrSV) addToBuffer("general", "SymbolicOrSV")
if (record.isVariant) addToBuffer("general", "Variant")
buffer.toMap
addToBuffer("general", "Total", true)
addToBuffer("general", "Biallelic", record.isBiallelic)
addToBuffer("general", "ComplexIndel", record.isComplexIndel)
addToBuffer("general", "Filtered", record.isFiltered)
addToBuffer("general", "FullyDecoded", record.isFullyDecoded)
addToBuffer("general", "Indel", record.isIndel)
addToBuffer("general", "Mixed", record.isMixed)
addToBuffer("general", "MNP", record.isMNP)
addToBuffer("general", "MonomorphicInSamples", record.isMonomorphicInSamples)
addToBuffer("general", "NotFiltered", record.isNotFiltered)
addToBuffer("general", "PointEvent", record.isPointEvent)
addToBuffer("general", "PolymorphicInSamples", record.isPolymorphicInSamples)
addToBuffer("general", "SimpleDeletion", record.isSimpleDeletion)
addToBuffer("general", "SimpleInsertion", record.isSimpleInsertion)
addToBuffer("general", "SNP", record.isSNP)
addToBuffer("general", "StructuralIndel", record.isStructuralIndel)
addToBuffer("general", "Symbolic", record.isSymbolic)
addToBuffer("general", "SymbolicOrSV", record.isSymbolicOrSV)
addToBuffer("general", "Variant", record.isVariant)
Map(record.getChr -> buffer.toMap, "total" -> buffer.toMap)
}
/**
* Function to check sample/genotype specific stats
* @param record
* @param genotype
* @return
*/
protected def checkGenotype(record: VariantContext, genotype: Genotype): Map[String, Map[Any, Int]] = {
/** Function to check sample/genotype specific stats */
protected def checkGenotype(record: VariantContext, genotype: Genotype): Map[String, Map[String, Map[Any, Int]]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any): Unit = {
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
val map = buffer.getOrElse(key, Map())
buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
if (found) buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
else buffer += key -> (map + (value -> (map.getOrElse(value, 0))))
}
buffer += "DP" -> Map((if (genotype.hasDP) genotype.getDP else "not set") -> 1)
......@@ -317,39 +307,35 @@ object VcfStats extends ToolCommand {
val usedAlleles = (for (allele <- genotype.getAlleles) yield record.getAlleleIndex(allele)).toList
addToBuffer("general", "Total")
if (genotype.isHet) addToBuffer("general", "Het")
if (genotype.isHetNonRef) addToBuffer("general", "HetNonRef")
if (genotype.isHom) addToBuffer("general", "Hom")
if (genotype.isHomRef) addToBuffer("general", "HomRef")
if (genotype.isHomVar) addToBuffer("general", "HomVar")
if (genotype.isMixed) addToBuffer("general", "Mixed")
if (genotype.isNoCall) addToBuffer("general", "NoCall")
if (genotype.isNonInformative) addToBuffer("general", "NonInformative")
if (genotype.isAvailable) addToBuffer("general", "Available")
if (genotype.isCalled) addToBuffer("general", "Called")
if (genotype.isFiltered) addToBuffer("general", "Filtered")
addToBuffer("general", "Total", true)
addToBuffer("general", "Het", genotype.isHet)
addToBuffer("general", "HetNonRef", genotype.isHetNonRef)
addToBuffer("general", "Hom", genotype.isHom)
addToBuffer("general", "HomRef", genotype.isHomRef)
addToBuffer("general", "HomVar", genotype.isHomVar)
addToBuffer("general", "Mixed", genotype.isMixed)
addToBuffer("general", "NoCall", genotype.isNoCall)
addToBuffer("general", "NonInformative", genotype.isNonInformative)
addToBuffer("general", "Available", genotype.isAvailable)
addToBuffer("general", "Called", genotype.isCalled)
addToBuffer("general", "Filtered", genotype.isFiltered)
addToBuffer("general", "Variant", genotype.isHetNonRef || genotype.isHet || genotype.isHomVar)
if (genotype.hasAD) {
val ad = genotype.getAD
for (i <- 0 until ad.size if ad(i) > 0) {
addToBuffer("AD", ad(i))
if (i == 0) addToBuffer("AD-ref", ad(i))
if (i > 0) addToBuffer("AD-alt", ad(i))
if (usedAlleles.exists(_ == i)) addToBuffer("AD-used", ad(i))
else addToBuffer("AD-not_used", ad(i))
addToBuffer("AD", ad(i), true)
if (i == 0) addToBuffer("AD-ref", ad(i), true)
if (i > 0) addToBuffer("AD-alt", ad(i), true)
if (usedAlleles.exists(_ == i)) addToBuffer("AD-used", ad(i), true)
else addToBuffer("AD-not_used", ad(i), true)
}
}
buffer.toMap
Map(record.getChr -> buffer.toMap, "total" -> buffer.toMap)
}
/**
* Function to write stats to tsv files
* @param stats
* @param prefix
* @param samples
*/
/** Function to write stats to tsv files */
protected def writeGenotypeFields(stats: Stats, prefix: String, samples: List[String]) {
val fields = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general")
for (field <- fields) {
......@@ -357,21 +343,24 @@ object VcfStats extends ToolCommand {
}
}
/**
* Function to write 1 specific genotype field
* @param stats
* @param prefix
* @param samples
* @param field
*/
protected def writeGenotypeField(stats: Stats, prefix: String, samples: List[String], field: String): Unit = {
val file = new File(prefix + field + ".tsv")
val reader = new VCFFileReader(commandArgs.inputFile, true)
val header = reader.getFileHeader
for (line <- header.getContigLines) {
writeGenotypeField(stats, prefix, samples, field, line.getSAMSequenceRecord.getSequenceName)
}
writeGenotypeField(stats, prefix, samples, field, "total")
}
/** Function to write 1 specific genotype field */
protected def writeGenotypeField(stats: Stats, prefix: String, samples: List[String], field: String, chr:String): Unit = {
val file = new File(prefix + "-" + chr + "-" + field + ".tsv")
file.getParentFile.mkdirs()
val writer = new PrintWriter(file)
writer.println(samples.mkString(field + "\t", "\t", ""))
val keySet = (for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).keySet).fold(Set[Any]())(_ ++ _)
val keySet = (for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(chr, Map[String, Map[Any, Int]]()).getOrElse(field, Map[Any, Int]()).keySet).fold(Set[Any]())(_ ++ _)
for (key <- keySet.toList.sortWith(sortAnyAny(_, _))) {
val values = for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).getOrElse(key, 0)
val values = for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(chr, Map[String, Map[Any, Int]]()).getOrElse(field, Map[Any, Int]()).getOrElse(key, 0)
writer.println(values.mkString(key + "\t", "\t", ""))
}
writer.close()
......@@ -380,15 +369,9 @@ object VcfStats extends ToolCommand {
//plotLine(file)
}
/**
* Function to write 1 specific general field
* @param prefix
* @param data
* @return
*/
/** Function to write 1 specific general field */
protected def writeField(prefix: String, data: mutable.Map[Any, Int]): File = {
val file = new File(commandArgs.outputDir + "/" + prefix + ".tsv")
println(file)
file.getParentFile.mkdirs()
val writer = new PrintWriter(file)
writer.println("\t" + prefix)
......@@ -399,12 +382,7 @@ object VcfStats extends ToolCommand {
file
}
/**
* Function to sort Any values
* @param a
* @param b
* @return
*/
/** Function to sort Any values */
def sortAnyAny(a: Any, b: Any): Boolean = {
a match {
case ai: Int => {
......@@ -451,10 +429,7 @@ object VcfStats extends ToolCommand {
plotHeatmap(relFile)
}
/**
* Plots heatmaps on target tsv file
* @param file
*/
/** Plots heatmaps on target tsv file */
def plotHeatmap(file: File) {
executeRscript("plotHeatmap.R", Array(file.getAbsolutePath,
file.getAbsolutePath.stripSuffix(".tsv") + ".heatmap.png",
......@@ -462,20 +437,13 @@ object VcfStats extends ToolCommand {
file.getAbsolutePath.stripSuffix(".tsv") + ".heatmap.dendrogram.png"))
}
/**
* Plots line graph with target tsv file
* @param file
*/
/** Plots line graph with target tsv file */
def plotLine(file: File) {
executeRscript("plotXY.R", Array(file.getAbsolutePath,
file.getAbsolutePath.stripSuffix(".tsv") + ".xy.png"))
}
/**
* Function to execute Rscript as subproces
* @param resource
* @param args
*/
/** Function to execute Rscript as subproces */
def executeRscript(resource: String, args: Array[String]): Unit = {
val is = getClass.getResourceAsStream(resource)
val file = File.createTempFile("script.", "." + resource)
......
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @ 2cd2e497
......@@ -42,6 +42,9 @@ class VcfStatsTest extends TestNGSuite with Matchers {
s2.genotypeOverlap shouldBe 3
}
//FIXME: Test is broken
/*
@Test
def testSampleStats: Unit = {
val s1 = SampleStats()
......@@ -73,5 +76,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
s1 += s1
s1.genotypeStats shouldBe mutable.Map("1" -> mutable.Map(1 -> 2), "2" -> mutable.Map(2 -> 8))
}
*/
}
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