Commit c405c4bb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'develop' into feature-merge_alleles

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
parents b8905325 df33687d
......@@ -37,7 +37,8 @@ object BiopetExecutable extends Logging {
nl.lumc.sasc.biopet.tools.SageCountFastq,
nl.lumc.sasc.biopet.tools.SageCreateLibrary,
nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
nl.lumc.sasc.biopet.tools.MergeAlleles)
nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.SamplesTsvToJson)
)
/**
......
......@@ -199,4 +199,28 @@ object Config extends Logging {
return None
}
}
def mapToJson(map: Map[String, Any]): Json = {
map.foldLeft(jEmptyObject)((acc, kv) => (kv._1 := {
kv._2 match {
case m: Map[_, _] => mapToJson(m.map(m => m._1.toString -> anyToJson(m._2)))
case _ => anyToJson(kv._2)
}
}) ->: acc)
}
def anyToJson(any: Any): Json = {
any match {
case j: Json => j
case m: Map[_, _] => mapToJson(m.map(m => m._1.toString -> anyToJson(m._2)))
case l: List[_] => Json.array(l.map(anyToJson(_)): _*)
case n: Int => Json.jNumberOrString(n)
case n: Double => Json.jNumberOrString(n)
case n: Long => Json.jNumberOrString(n)
case n: Short => Json.jNumberOrString(n)
case n: Float => Json.jNumberOrString(n)
case n: Byte => Json.jNumberOrString(n)
case _ => jString(any.toString)
}
}
}
\ No newline at end of file
package nl.lumc.sasc.biopet.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommand
import scala.io.Source
import nl.lumc.sasc.biopet.core.config.Config
object SamplesTsvToJson extends ToolCommand {
case class Args(inputFiles: List[File] = Nil) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('i', "inputFiles") required () unbounded () valueName ("<file>") action { (x, c) =>
c.copy(inputFiles = x :: c.inputFiles)
} text ("Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed")
}
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val fileMaps = for (inputFile <- commandArgs.inputFiles) yield {
val reader = Source.fromFile(inputFile)
val lines = reader.getLines.toList
val header = lines.head.split("\t")
val sampleColumn = header.indexOf("sample")
val libraryColumn = header.indexOf("library")
if (sampleColumn == -1) throw new IllegalStateException("sample column does not exist in: " + inputFile)
val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
val values = tsvLine.split("\t")
val sample = values(sampleColumn)
val library = if (libraryColumn != -1) values(libraryColumn) else null
val valuesMap = (for (t <- 0 until values.size if t != sampleColumn if t != libraryColumn) yield (header(t) -> values(t))).toMap
val map: Map[String, Any] = if (library != null) {
Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
} else {
Map("samples" -> Map(sample -> valuesMap))
}
map
}
librariesValues.foldLeft(Map[String, Any]())((acc, kv) => Config.mergeMaps(acc, kv))
}
val map = fileMaps.foldLeft(Map[String, Any]())((acc, kv) => Config.mergeMaps(acc, kv))
val json = Config.mapToJson(map)
println(json.spaces2)
}
}
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