From 9cb010e94e60504548d66f7d7e75661e3533f5ab Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 May 2016 13:27:23 +0200
Subject: [PATCH] Add gtf to refflat
---
.../nl/lumc/sasc/biopet/extensions/Awk.scala | 41 +++++++++++++++++++
.../biopet/extensions/GtfToGenePred.scala | 39 ++++++++++++++++++
.../generateindexes/GenerateIndexes.scala | 7 +++-
3 files changed, 85 insertions(+), 2 deletions(-)
create mode 100644 biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
create mode 100644 biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
new file mode 100644
index 000000000..594e6f564
--- /dev/null
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala
@@ -0,0 +1,41 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvan_thof on 17-5-16.
+ */
+class Awk(val root: Configurable) extends BiopetCommandLineFunction with Version {
+ executable = config("exe", default = "awk", freeVar = false)
+
+ def versionCommand: String = executable + " --version"
+
+ def versionRegex: Regex = """(GNU Awk \d+\.\d+\.\d+)""".r
+
+ @Input(required = false)
+ var input: File = _
+
+ @Output
+ var output: File = _
+
+ var command: String = _
+
+ def cmdLine = executable +
+ required(command) +
+ (if (inputAsStdin) "" else required(input)) +
+ (if (outputAsStsout) "" else " > " + required(output))
+}
+
+object Awk {
+ def apply(root: Configurable, command: String): Awk = {
+ val awk = new Awk(root)
+ awk.command = command
+ awk
+ }
+}
\ No newline at end of file
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
new file mode 100644
index 000000000..3593ef84b
--- /dev/null
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala
@@ -0,0 +1,39 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvan_thof on 17-5-16.
+ */
+class GtfToGenePred(val root: Configurable) extends BiopetCommandLineFunction {
+ executable = config("exe", default = "gtfToGenePred", freeVar = false)
+
+ @Input
+ var inputGtfs: List[File] = Nil
+
+ @Output
+ var outputGenePred: File = _
+
+ @Output
+ var infoOut: Option[File] = None
+
+ var genePredExt: Boolean = config("gene _pred _ext", default = false)
+ var allErrors: Boolean = config("all_errors", default = false)
+ var impliedStopAfterCds: Boolean = config("implied_stop_after_cds", default = false)
+ var simple: Boolean = config("simple", default = false)
+ var geneNameAsName2: Boolean = config("gene _name_as_name2", default = false)
+
+ def cmdLine = executable +
+ conditional(genePredExt, "-genePredExt") +
+ conditional(allErrors, "-allErrors") +
+ optional("-infoOut", infoOut) +
+ conditional(allErrors, "-allErrors") +
+ conditional(impliedStopAfterCds, "-impliedStopAfterCds") +
+ conditional(simple, "-simple") +
+ conditional(geneNameAsName2, "-geneNameAsName2") +
+ (if (outputAsStsout) "" else " > " + required(outputGenePred))
+}
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
index f4a0e0406..38eb6178c 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -208,9 +208,12 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val refFlatFile: Option[File] = gtfFile.map { gtf =>
val refFlat = new File(gtf + ".refFlat")
- //TODO: gtf to refFlat conversion
+ val gtfToGenePred = new GtfToGenePred(this)
+ gtfToGenePred.inputGtfs :+= gtf
- outputConfig += "ribosome_refflat" -> refFlat
+ add(gtfToGenePred | Awk(this, """{ print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }""") > refFlat)
+
+ outputConfig += "annotation_refflat" -> refFlat
refFlat
}
--
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