From d1bd5949024f8482b04fac337e019fb9262016ef Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 31 Aug 2015 16:50:02 +0200
Subject: [PATCH] Refactoring SummaryToTsv to make it more testable Removing
extraneous output flag (wasn't used) Better help messages And mode validation
---
.../lumc/sasc/biopet/tools/SummaryToTsv.scala | 44 ++++++++++++++-----
1 file changed, 32 insertions(+), 12 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
index 398a9b73f..9374e9242 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
+import java.nio.file.Paths
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.summary.Summary
@@ -35,15 +36,24 @@ object SummaryToTsv extends ToolCommand {
opt[File]('s', "summary") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(summary = x)
}
- opt[File]('o', "output") maxOccurs 1 unbounded () valueName "<file>" action { (x, c) =>
- c.copy(outputFile = Some(x))
- }
- opt[String]('p', "path") required () unbounded () valueName "<value>" action { (x, c) =>
+ opt[String]('p', "path") required () unbounded () valueName "<string>" action { (x, c) =>
c.copy(values = c.values ::: x :: Nil)
- }
+ } text
+ """
+ |String that determines the values extracted from the summary. Should be of the format:
+ |<header_name>=<namespace>:<lower_namespace>:<even_lower_namespace>...
+ """.stripMargin
opt[String]('m', "mode") maxOccurs 1 unbounded () valueName "<root|sample|lib>" action { (x, c) =>
c.copy(mode = x)
- }
+ } validate {
+ x => if (Set("root","sample","lib").contains(x)) success else failure("Unsupported mode")
+ } text
+ """
+ |Determines on what level to aggregate data.
+ |root: at the root level
+ |sample: at the sample level
+ |lib: at the library level
+ """.stripMargin
}
@@ -56,14 +66,14 @@ object SummaryToTsv extends ToolCommand {
val paths = cmdArgs.values.map(x => {
val split = x.split("=", 2)
split(0) -> split(1).split(":")
- })
+ }).toMap
- val values = fetchValues(summary, paths.toMap, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
+ val values = fetchValues(summary, paths, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
- println(paths.map(_._1).mkString("\t", "\t", ""))
+ println(createHeader(paths))
for (lineId <- values.head._2.keys) {
- println(paths.map(x => values(x._1)(lineId).getOrElse("")).mkString(lineId + "\t", "\t", ""))
+ println(createLine(paths, values, lineId))
}
}
@@ -71,9 +81,19 @@ object SummaryToTsv extends ToolCommand {
sample: Boolean = false,
lib: Boolean = false) = {
for ((name, path) <- paths) yield name -> {
- if (lib) summary.getLibraryValues(path: _*).map(a => (a._1._1 + "-" + a._1._2) -> a._2)
- else if (sample) summary.getSampleValues(path: _*)
+ if (lib) {
+ summary.getLibraryValues(path: _*).map(a => (a._1._1 + "-" + a._1._2) -> a._2)
+ } else if (sample) summary.getSampleValues(path: _*)
else Map("value" -> summary.getValue(path: _*))
}
}
+
+ def createHeader(paths: Map[String, Array[String]]): String = {
+ paths.map(_._1).mkString("\t", "\t", "")
+ }
+
+ def createLine(paths: Map[String, Array[String]],
+ values: Map[String, Map[String, Option[Any]]], lineId: String): String = {
+ paths.map(x => values(x._1)(lineId).getOrElse("")).mkString(lineId + "\t", "\t", "")
+ }
}
--
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