Merge branch 'feature-sample_regex' into 'develop'

Added regex option



See merge request !458

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala

@@ -6,6 +6,7 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
+import scala.util.matching.Regex
 
 /**
  * This tool will find all pairs above a cutoff in a data table
@@ -17,7 +18,9 @@ object FindOverlapMatch extends ToolCommand {
   case class Args(inputMetrics: File = null,
                   outputFile: Option[File] = None,
                   cutoff: Double = 0.0,
-                  filterSameNames: Boolean = true) extends AbstractArgs
+                  filterSameNames: Boolean = true,
+                  rowSampleRegex: Option[Regex] = None,
+                  columnSampleRegex: Option[Regex] = None) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('i', "input") required () unbounded () valueName "<file>" action { (x, c) =>
@@ -32,7 +35,12 @@ object FindOverlapMatch extends ToolCommand {
     opt[Unit]("use_same_names") unbounded () valueName "<value>" action { (x, c) =>
       c.copy(filterSameNames = false)
     } text "Do not compare samples with the same name"
-
+    opt[String]("rowSampleRegex") unbounded () valueName "<regex>" action { (x, c) =>
+      c.copy(rowSampleRegex = Some(x.r))
+    } text "Samples in the row should match this regex"
+    opt[String]("columnSampleRegex") unbounded () valueName "<regex>" action { (x, c) =>
+      c.copy(columnSampleRegex = Some(x.r))
+    } text "Samples in the column should match this regex"
   }
 
   /**
@@ -58,19 +66,19 @@ object FindOverlapMatch extends ToolCommand {
       case _          => sys.process.stdout
     }
 
-    for (i1 <- samplesColumnHeader) {
+    for (columnSample <- samplesColumnHeader if cmdArgs.columnSampleRegex.map(_.findFirstIn(columnSample._1).isDefined).getOrElse(true)) {
       val buffer = ListBuffer[(String, Double)]()
-      for (i2 <- samplesRowHeader) {
-        val value = data(i1._2)(i2._2).toDouble
-        if (value >= cmdArgs.cutoff && (!cmdArgs.filterSameNames || i1._2 != i2._2)) {
-          buffer.+=((i2._1, value))
+      for (rowSample <- samplesRowHeader if cmdArgs.rowSampleRegex.map(_.findFirstIn(rowSample._1).isDefined).getOrElse(true)) {
+        val value = data(columnSample._2)(rowSample._2).toDouble
+        if (value >= cmdArgs.cutoff && (!cmdArgs.filterSameNames || columnSample._2 != rowSample._2)) {
+          buffer.+=((rowSample._1, value))
         }
       }
       if (buffer.nonEmpty) overlap += 1
       else noOverlap += 1
       if (buffer.size > 1) multiOverlap += 1
 
-      writer.println(s"${i1._1}\t${buffer.mkString("\t")}")
+      writer.println(s"${columnSample._1}\t${buffer.mkString("\t")}")
     }
     logger.info(s"$overlap found")
     logger.info(s"no $noOverlap found")