updated examples

Author: holgerbrandl

examples/more_examples.sh

@@ -0,0 +1,72 @@
+
+
+kscript - test2.fastq <<"EOF"
+java.io.File(args[0]).useLines {
+    it.map {
+        if (!it.startsWith(">")) it else "huhu" + it
+    }.forEach { println(it) }
+}
+EOF
+
+
+
+
+kscript - <<"EOF"
+println("getting started")
+generateSequence() { readLine() }.map {
+    if (!it.startsWith(">")) it else
+        "huhu" + it
+}.forEach { println(it) }
+EOF
+
+
+head -n 1000 test.fastq > test2.fastq
+
+
+## how use stdin but still use heredoc for cod
+kscript - test2.fastq <(echo <<"EOF"
+println("getting started")
+//generateSequence() { readLine() }.map {
+File(args[0]).readLines().map {
+    if (!it.startsWith(">")) it else
+        "huhu" + it
+}.forEach { println(it) }
+EOF
+)
+
+
+
+## todo provide picard tools examples
+http://mvnrepository.com/artifact/com.github.broadinstitute/picard/2.5.0
+potentially like
+https://www.biostars.org/p/52698/
+
+
+## simplified line streaming
+
+
+
+fun main(args: Array<String>) {
+    kutils.KscriptHelpers.processStdin { "huhu" + it }
+}
+
+
+kscript -s '
+//DEPS de.mpicbg.scicomp:kutils:0.2-SNAPSHOT
+kutils.KscriptHelpers.processStdin { "huhu" + it }
+
+'
+
+## todo streamline further by using simple code wrapper for (see https://github.com/holgerbrandl/kscript/issues/9)
+kscript -st '"huhu" + it'
+
+
+## REPL test: Filter-Join fasta files by ID
+kotlinc -classpath $(expandcp.kts de.mpicbg.scicomp:kutils:0.2-SNAPSHOT) 
+<<"EOF"
+
+
+kutils.KscriptHelpers.processStdin { "huhu" + it }
+kscript 
+
+EOF

examples/scratchpad.kts

@@ -0,0 +1,24 @@
+#!/usr/bin/env kscript
+
+import de.mpicbg.scicomp.kscript.processLines
+
+println("ok")
+println(args.joinToString())
+
+// test
+
+
+//generateSequence() { readLine() }.map {
+//File(args[0]).readLines().map {}
+
+java.io.File(args[0]).useLines {
+    it.map {
+        if (!it.startsWith(">")) {
+            it.substring(0, 20)
+        } else it
+    }.forEach { println(it) }
+}
+
+
+java.io.File(args[0]).processLines { it + "foo" }
+

examples/test.kts

@@ -6,6 +6,10 @@
     <groupId>kscript</groupId>
     <version>1.0-SNAPSHOT</version>
 
+    <properties>
+        <kotlin.version>1.0.3</kotlin.version>
+    </properties>
+
 
     <dependencies>
         <dependency>
@@ -17,8 +21,53 @@
         <dependency>
             <groupId>de.mpicbg.scicomp</groupId>
             <artifactId>kutils</artifactId>
-            <version>0.2-SNAPSHOT</version>
+            <version>0.2</version>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-stdlib</artifactId>
+            <version>${kotlin.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-test</artifactId>
+            <version>${kotlin.version}</version>
+            <scope>test</scope>
         </dependency>
 
     </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.jetbrains.kotlin</groupId>
+                <artifactId>kotlin-maven-plugin</artifactId>
+                <version>${kotlin.version}</version>
+                <executions>
+                    <execution>
+                        <id>compile</id>
+                        <phase>compile</phase>
+                        <goals>
+                            <goal>compile</goal>
+                        </goals>
+                        <configuration>
+                            <sourceDirs>
+                                <source>examples</source>
+                                <source></source>
+                            </sourceDirs>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>test-compile</id>
+                        <phase>test-compile</phase>
+                        <goals>
+                            <goal>test-compile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+
 </project>