create TileGenome command line version

This tool did not implement JFrame elements in the script class so the
CLI implementation did not need to create an src/window_interface/*/
TileGenomeOutput class. As a result, just the following files were
affected:

window_interface/*Window
	-adjust output argument when initializing script class to be
		full filename and not just directory
script/*
	-use output as filename rather than directory name
cli/*
	-call appropriate script class
	-write up picocli parsing objects
	-write up validateInput() method to check inputs and write
		messages for the user

Author: owlang

src/cli/Peak_Analysis/TileGenomeCLI.java

@@ -12,7 +12,7 @@
 
 import objects.ToolDescriptions;
 import util.ExtensionFileFilter;
-//import scripts.Peak_Analysis.TileGenome;
+import scripts.Peak_Analysis.TileGenome;
 
 /**
 	Peak_AnalysisCLI/TileGenomeCLI
@@ -24,6 +24,16 @@
 	exitCodeOnExecutionException = 1)
 public class TileGenomeCLI implements Callable<Integer> {
 
+	@Parameters( index = "0", description = "reference genome [sacCer3_cegr|hg19|hg19_contigs|mm10]")
+	private String genomeName;
+	
+	@Option(names = {"-o", "--output"}, description = "Specify output directory (default = current working directory), file name will be genome_tiles_<genomeName>_<window>bp.<ext>")
+	private File output = null;
+	@Option(names = {"-f", "--gff"}, description = "file format output as GFF (default format as BED)")
+	private boolean formatIsBed = true;
+	@Option(names = {"-w", "--window"}, description = "window size in bp (default=200)")
+	private int window = 200;
+	
 	@Override
 	public Integer call() throws Exception {
 		System.err.println( ">TileGenomeCLI.call()" );
@@ -34,16 +44,48 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		//SEStats.getSEStats( output, bamFile, null );
+		TileGenome script_obj = new TileGenome(genomeName, window, formatIsBed, output);
+		script_obj.execute();
 
-		//System.err.println("Calculations Complete");
+		System.err.println( "Genomic Tiling Complete." );
 		return(0);
 	}
 
 	private String validateInput() throws IOException {
 		String r = "";
-		//validate input here
-		//append messages to the user to `r`
+		
+		//check input genomes are valid
+		if(genomeName.equals("sacCer3_cegr") || genomeName.equals("hg19") || genomeName.equals("hg19_contigs") || genomeName.equals("mm10") ){
+// 			System.err.println("Input genome is valid");
+		}else{
+			r += "(!)Invalid genomeName selected(" +genomeName+ "), please select from one of the provided genomes: sacCer3_cegr, hg19, hg19_contigs, and mm10\n";
+		}
+		String ext = "gff";
+		if(formatIsBed){ ext = "bed"; }
+		//set default output filename
+		if(output==null){
+			output = new File(genomeName + "_" + window + "bp." + ext);
+		//check output filename is valid
+		}else{
+			//check ext
+			try{
+				if(!ext.equals(ExtensionFileFilter.getExtension(output))){
+					r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
+				}
+			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
+			//check directory
+			if(output.getParent()==null){
+	// 			System.err.println("default to current directory");
+			} else if(!new File(output.getParent()).exists()){
+				r += "(!)Check output directory exists: " + output.getParent() + "\n";
+			}
+		}
+		
+		//check window size
+		if( window<1 ){
+			r += "(!)Window size needs to be a positive integer.\n";
+		}
+		
 		return(r);
 	}
 }

src/scripts/Peak_Analysis/TileGenome.java

@@ -29,8 +29,8 @@ public void execute() throws IOException {
 
 	    String fileName = GENOME + "_" + windowSize + "bp" + EXTENSION;
 		PrintStream OUT = null;
-		if(OUTPUT == null) OUT = new PrintStream(fileName);
-	    else OUT = new PrintStream(OUTPUT + File.separator + fileName);
+		if(OUTPUT == null) OUT = new PrintStream(new File(fileName));
+	    else OUT = new PrintStream(OUTPUT);
 
 		for(int x = 0; x < coord.getChrom().size(); x++) {
 			String CHROM = coord.getChrom().get(x);

src/window_interface/Peak_Analysis/TileGenomeWindow.java

@@ -53,7 +53,17 @@ public Void doInBackground() throws IOException, InterruptedException {
 	        		} else if(Integer.parseInt(txtSize.getText()) < 1) {
 	    				JOptionPane.showMessageDialog(null, "Invalid Window Size Entered!!!");
 	        		} else {
-	        			TileGenome generate = new TileGenome((String)cmbGenome.getSelectedItem(), Integer.parseInt(txtSize.getText()), rdbtnBed.isSelected(), OUTPUT_PATH);
+	        			boolean bedStatus = rdbtnBed.isSelected();
+						String randomName = (String)cmbGenome.getSelectedItem() + "_" + Integer.parseInt(txtSize.getText()) + "bp";
+						if(bedStatus){ randomName += ".bed"; }
+						else{ randomName += ".gff"; }
+						File OUTFILE;
+						if(OUTPUT_PATH != null){
+							OUTFILE = new File(OUTPUT_PATH + File.separator + randomName);
+						}else{
+							OUTFILE = new File(randomName);
+						}
+	        			TileGenome generate = new TileGenome((String)cmbGenome.getSelectedItem(), Integer.parseInt(txtSize.getText()), bedStatus, OUTFILE);
 	        			generate.execute();
 	    				JOptionPane.showMessageDialog(null, "Genomic Tiling Complete");
 	        		}