add CLI to ShiftCoord

CLI for ShiftCoord script for #92

Author: owlang

src/cli/Coordinate_Manipulation/ShiftCoordCLI.java

@@ -0,0 +1,91 @@
+package cli.Coordinate_Manipulation;
+
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+
+import java.util.concurrent.Callable;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.FileNotFoundException;
+
+import objects.ToolDescriptions;
+import util.CDTUtilities;
+import util.ExtensionFileFilter;
+import scripts.Coordinate_Manipulation.ShiftCoord;
+
+/**
+	Coordinate_ManipulationCLI/ShiftCoordCLI
+*/
+@Command(name = "shift-coord", mixinStandardHelpOptions = true,
+	description = ToolDescriptions.shift_coordinate_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
+	sortOptions = false,
+	exitCodeOnInvalidInput = 1,
+	exitCodeOnExecutionException = 1)
+public class ShiftCoordCLI implements Callable<Integer> {
+	
+	@Parameters( index = "0", description = "the coordinate file (BED/GFF format) to shift")
+	private File input;
+	
+	@Option(names = {"-o", "--output"}, description = "specify output filepath (default input filename with _shiftXXXbp.bed/gff)")
+	private String outputFilepath = null;
+	@Option(names = {"-t", "--shift"}, description = "shift distance in bp, upstream  < 0 and downstream > 0 (default=0)")
+	private int shift = 0;
+	@Option(names = {"-u", "--unstranded"}, description = "don't force strandedness (default=forced)")
+	private boolean stranded = true;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
+	@Option(names = {"--gff"}, description = "input is GFF format (default=BED format)")
+	private boolean isGFF = false;
+
+	@Override
+	public Integer call() throws Exception {
+		System.err.println( ">ShiftCoord.call()" );
+		String validate = validateInput();
+		if(!validate.equals("")){
+			System.err.println( validate );
+			System.err.println("Invalid input. Check usage using '-h' or '--help'");
+			System.exit(1);
+		}
+
+		if(isGFF) {
+			ShiftCoord.shiftGFFInterval(new File(outputFilepath), input, shift, stranded, gzOutput);
+		} else {
+			ShiftCoord.shiftBEDInterval(new File(outputFilepath), input, shift, stranded, gzOutput);
+		}
+		
+		System.err.println("Shift Complete");
+		return(0);
+	}
+	
+	private String validateInput() throws IOException {
+		String r = "";
+		
+		//check inputs exist
+		if(!input.exists()){
+			r += "(!)BED/GFF file does not exist: " + input.getName() + "\n";
+		}
+		if(!"".equals(r)){ return(r); }
+		
+		//set default output filename
+		if(outputFilepath==null){
+			String SUFFIX = shift < 0 ? "_shift" + shift + "bp." : "_shift+" + shift + "bp.";
+			SUFFIX += isGFF ? "gff" : "bed";
+			SUFFIX += gzOutput ? ".gz" : "";
+			outputFilepath = ExtensionFileFilter.stripExtension(input) + SUFFIX;
+		//check output filename is valid
+		}else{
+			//no extension check
+			//check directory
+			File BASEFILE = new File(outputFilepath);
+			if(BASEFILE.getParent()==null){
+// 				System.err.println("default to current directory");
+			} else if(!new File(BASEFILE.getParent()).exists()){
+				r += "(!)Check output directory exists: " + BASEFILE.getParent() + "\n";
+			}
+		}
+		return(r);
+	}
+}

src/main/ScriptManager.java

@@ -22,6 +22,8 @@
 import cli.BAM_Statistics.PEStatsCLI;
 import cli.BAM_Statistics.SEStatsCLI;
 
+import cli.Coordinate_Manipulation.ShiftCoordCLI;
+
 import cli.Coordinate_Manipulation.BED_Manipulation.BEDtoGFFCLI;
 import cli.Coordinate_Manipulation.BED_Manipulation.ExpandBEDCLI;
 import cli.Coordinate_Manipulation.BED_Manipulation.SortBEDCLI;
@@ -149,6 +151,7 @@ class BAM_StatisticsCLI extends SubcommandCLI {}
 
 @Command(name = "coordinate-manipulation",
 		subcommands = {
+			ShiftCoordCLI.class,
 			BEDtoGFFCLI.class,
 			ExpandBEDCLI.class,
 			SortBEDCLI.class,