started kotlin docopt facade

Author: holgerbrandl

build.gradle

@@ -26,6 +26,7 @@ repositories {
 dependencies {
 //    compileOnly "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_version"
     compile "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_version"
+    compile "com.offbytwo:docopt:0.6.0.20150202"
 
     testCompile 'junit:junit:4.11'
     testCompile "io.kotlintest:kotlintest:2.0.1"

src/main/kotlin/kscript/ArgUtil.kt

@@ -0,0 +1,29 @@
+package kscript
+
+import org.docopt.Docopt
+import java.io.File
+
+/**
+ * Helpers to build CLIs with kscript and docopt
+ *
+ * @author Holger Brandl
+ */
+
+/** Simple Kotlin facade for org.docopt.Docopt.Docopt(java.lang.String) .*/
+class DocOpt(args: Array<String>, val usage: String) {
+
+    val myDO by lazy {
+        Docopt(usage).parse(args.toList()).map {
+            it.key.removePrefix("--").replace("[<>]".toRegex(), "") to it.value?.toString()
+        }.toMap()
+    }
+
+    fun getString(key: String) = myDO[key]!!
+    fun getStrings(key: String) = myDO[key]!!
+
+    fun getInt(key: String) = myDO[key]!!.toInt()
+
+    fun getNumber(key: String) = myDO[key]!!.toFloat()
+
+    fun getBoolean(key: String) = myDO[key]!!.toBoolean()
+}

src/main/kotlin/kscript/DocOpt.kt

@@ -0,0 +1,37 @@
+package kscript.test
+
+import io.kotlintest.matchers.shouldBe
+import io.kotlintest.specs.StringSpec
+import kscript.DocOpt
+
+/**
+ * @author Holger Brandl
+ */
+
+
+class DocOptTest : StringSpec() { init {
+
+    val args = "-n 7 --pc-only --gtf my.gtf a.fastq b.fastq".split(" ").toTypedArray()
+
+    val usage = """
+Use star to align fastq files against a genome
+Usage: star_align.kts [options] <igenome> <fastq_files>...
+
+Options:
+ --gtf <gtfFile>        Custom gtf file instead of igenome bundled copy
+ --pc-only              Use protein coding genes only for mapping and quantification
+ -n --num-fragments     Fragment count used for processing [default: 5]
+"""
+
+    val docopt = DocOpt(args, usage)
+
+    docopt.getString("gtf") shouldBe "my.gtf"
+    docopt.getStrings("fastq_files") shouldBe arrayOf("a.fastq", "b.fastq")
+
+    docopt.getInt("fastq_files")
+    docopt.getNumber("num-fragments") shouldBe 7
+    docopt.getNumber("num-fragments") shouldBe 7
+    docopt.getNumber("-n")
+    docopt.getBoolean("pc-only") shouldBe true
+}
+}