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Commit 065bf160 authored by Peter van 't Hof's avatar Peter van 't Hof
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Implement new methods

parent a592e31b
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Showing with 36 additions and 177 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ 065bf160
......@@ -176,66 +176,17 @@ object BammetricsReport extends ReportBuilder {
libId: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) {
tsvWriter.println((for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) yield s"$sample-$lib")
.mkString("library\t", "\t", ""))
} else {
sampleId match {
case Some(sample) => tsvWriter.println("\t" + sample)
case _ => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
}
}
var map: Map[Int, Map[String, Int]] = Map()
def fill(sample: String, lib: Option[String]): Unit = {
val insertSize = new SummaryValue(List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "insert_size"),
summary, Some(sample), lib).value.getOrElse(List())
val counts = new SummaryValue(List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "All_Reads.fr_count"),
summary, Some(sample), lib).value.getOrElse(List())
(insertSize, counts) match {
case (l: List[_], l2: List[_]) =>
l.zip(l2).foreach(i => {
val insertSize = i._1.toString.toInt
val count = i._2.toString.toInt
val old = map.getOrElse(insertSize, Map())
if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
else map += insertSize -> (old + (sample -> count))
})
case _ => throw new IllegalStateException("Must be a list")
}
}
def paths(name: String) = Map(
"insert_size" -> List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "insert_size"),
name -> List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "All_Reads.fr_count")
)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) fill(sample, Some(lib))
} else if (sampleId.isDefined) fill(sampleId.get, None)
else summary.samples.foreach(fill(_, None))
for ((insertSize, counts) <- map) {
tsvWriter.print(insertSize)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
} else {
for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
}
val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
.map { case (sample, lib) =>
getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
}
tsvWriter.println()
}
tsvWriter.close()
writeTableToTsv(tsvFile, mergeTables(tables.toArray, "insert_size"), "insert_size")
LinePlot(tsvFile, pngFile,
xlabel = Some("Insert size"),
......@@ -261,68 +212,17 @@ object BammetricsReport extends ReportBuilder {
libId: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) {
tsvWriter.println((for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) yield s"$sample-$lib")
.mkString("library\t", "\t", ""))
} else {
sampleId match {
case Some(sample) => tsvWriter.println("\t" + sample)
case _ => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
}
}
var map: Map[Int, Map[String, Long]] = Map()
def fill(sample: String, lib: Option[String]): Unit = {
val insertSize = new SummaryValue(List("bammetrics", "stats", "wgs", "histogram", "coverage"),
summary, Some(sample), lib).value.getOrElse(List())
val counts = new SummaryValue(List("bammetrics", "stats", "wgs", "histogram", "count"),
summary, Some(sample), lib).value.getOrElse(List())
(insertSize, counts) match {
case (l: List[_], l2: List[_]) =>
l.zip(l2).foreach(i => {
val insertSize = i._1.toString.toInt
val count = i._2.toString.toLong
val old = map.getOrElse(insertSize, Map())
if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
else map += insertSize -> (old + (sample -> count))
})
case _ => throw new IllegalStateException("Must be a list")
}
}
def paths(name: String) = Map(
"coverage" -> List("bammetrics", "stats", "wgs", "histogram", "coverage"),
name -> List("bammetrics", "stats", "wgs", "histogram", "count")
)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) fill(sample, Some(lib))
} else if (sampleId.isDefined) fill(sampleId.get, None)
else summary.samples.foreach(fill(_, None))
for ((insertSize, counts) <- map) {
tsvWriter.print(insertSize)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) {
tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
}
} else {
for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
}
val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
.map { case (sample, lib) =>
getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
}
tsvWriter.println()
}
tsvWriter.close()
writeTableToTsv(tsvFile, mergeTables(tables.toArray, "coverage"), "coverage")
LinePlot(tsvFile, pngFile,
xlabel = Some("Coverage"),
......@@ -348,68 +248,17 @@ object BammetricsReport extends ReportBuilder {
libId: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
if (libraryLevel) {
tsvWriter.println((for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) yield s"$sample-$lib")
.mkString("library\t", "\t", ""))
} else {
sampleId match {
case Some(sample) => tsvWriter.println("\t" + sample)
case _ => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
}
}
var map: Map[Int, Map[String, Double]] = Map()
def fill(sample: String, lib: Option[String]): Unit = {
val insertSize = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
summary, Some(sample), lib).value.getOrElse(List())
val counts = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage"),
summary, Some(sample), lib).value.getOrElse(List())
(insertSize, counts) match {
case (l: List[_], l2: List[_]) =>
l.zip(l2).foreach(i => {
val insertSize = i._1.toString.toInt
val count = i._2.toString.toDouble
val old = map.getOrElse(insertSize, Map())
if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
else map += insertSize -> (old + (sample -> count))
})
case _ => throw new IllegalStateException("Must be a list")
}
}
def paths(name: String) = Map(
"normalized_position" -> List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
name -> List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage")
)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) fill(sample, Some(lib))
} else if (sampleId.isDefined) fill(sampleId.get, None)
else summary.samples.foreach(fill(_, None))
for ((insertSize, counts) <- map) {
tsvWriter.print(insertSize)
if (libraryLevel) {
for (
sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
) {
tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
}
} else {
for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
}
val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
.map { case (sample, lib) =>
getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
}
tsvWriter.println()
}
tsvWriter.close()
writeTableToTsv(tsvFile, mergeTables(tables.toArray, "normalized_position"), "normalized_position")
LinePlot(tsvFile, pngFile,
xlabel = Some("Relative position"),
......@@ -418,6 +267,16 @@ object BammetricsReport extends ReportBuilder {
removeZero = true).runLocal()
}
private def getSampleLibraries(summary: Summary,
sampleId: Option[String] = None,
LibId: Option[String] = None,
libraryLevel: Boolean = false): List[(String, Option[String])] = {
if (LibId.isDefined) require(sampleId.isDefined)
if (libraryLevel || LibId.isDefined)
for ((sample, libs) <- summary.libraries.toList; lib <- libs) yield (sample, Some(lib))
else for ((sample, libs) <- summary.libraries.toList) yield (sample, None)
}
def getTableFromSummary(summary: Summary,
paths: Map[String, List[String]],
sampleId: Option[String] = None,
......@@ -431,8 +290,8 @@ object BammetricsReport extends ReportBuilder {
pathValues
}
def mergeTables(tables: List[Map[String, Array[Any]]],
mergeColumn: String, defaultValue: Any = 0): Map[String, List[Any]] = {
def mergeTables(tables: Array[Map[String, Array[Any]]],
mergeColumn: String, defaultValue: Any = 0): Map[String, Array[Any]] = {
val keys = tables.flatMap(x => x(mergeColumn)).distinct
(for (table <- tables; (columnKey, columnValues) <- table if columnKey != mergeColumn) yield {
columnKey -> keys.map(x => table(mergeColumn).zip(columnValues).toMap.getOrElse(x, defaultValue))
......
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