New Tool: FRiX Calculator and restructure main GUI

src/main/java/scriptmanager/charts/Histogram.java

@@ -8,6 +8,8 @@
 import org.jfree.chart.ChartPanel;
 import org.jfree.chart.ChartUtils;
 import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.TickUnitSource;
+import org.jfree.chart.axis.ValueAxis;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.chart.plot.XYPlot;
 import org.jfree.chart.renderer.xy.StandardXYBarPainter;
@@ -21,6 +23,7 @@
  * 
  * @author William KM Lai
  * @see scriptmanager.scripts.BAM_Statistics.PEStats
+ * @see scriptmanager.scripts.Peak_Analysis.FRiXCalculator
  */
 public class Histogram {
 
@@ -120,4 +123,77 @@ private static JFreeChart createChart(IntervalXYDataset dataset) throws IOExcept
 
         return chart;
     }
+
+	/**
+	 * Plot a set of bar-style plots using the frequencies (y) of values (x)
+	 * parallel input arrays with title "FRiX", domain axis label "Tag Count
+	 * (reads)", and y-axis label "Frequency".
+	 * 
+	 * @param y      the list of frequencies
+	 * @param x      the list of values that have frequencies (same len as y)
+	 * @param name   the subtitle for the plot (FRiX - \<name\>)
+	 * @return the bar-style histogram chart
+	 * @throws IOException
+	 */
+	public static ChartPanel createFRiXBarChart(double[] y, int[] x, String name) throws IOException {
+		final XYSeries series = new XYSeries("Frequency");
+		for(int i = 0; i < x.length; i++) {
+			series.add((double)x[i], (double)y[i]);
+		}
+		final XYSeriesCollection dataset = new XYSeriesCollection(series);
+
+		JFreeChart chart = createFRiXChart(dataset, name);
+		final ChartPanel chartPanel = new ChartPanel(chart);
+		chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
+
+		return chartPanel;
+	}
+
+	/**
+	 * Helper method to turn a formatted dataset into a standard chart with specific
+	 * look configurations including hard coded titles, axis labels, orientation,
+	 * legend, tooltips, grid colors, etc) for the FRiX calculator tool.
+	 * 
+	 * @param dataset the formatted dataset to plot
+	 * @param name   the subtitle for the plot (FRiX - \<name\>)
+	 * @return the formatted and configured histogram chart
+	 * @throws IOException
+	 */
+	private static JFreeChart createFRiXChart(IntervalXYDataset dataset, String name) throws IOException {
+		final JFreeChart chart = ChartFactory.createXYBarChart(
+				"FRiX - " + name, // chart title
+				"Tag Count (reads)", // domain axis label
+				false, "Frequency", // range axis label
+				dataset, // data
+				PlotOrientation.VERTICAL, // orientation
+				true, // include legend
+				true, // tooltips
+				false // urls
+		);
+		XYPlot plot = (XYPlot) chart.getPlot();
+		// Set Histogram Color to Red
+		plot.getRenderer().setSeriesPaint(0, new Color(51, 51, 51));
+		plot.setBackgroundPaint(Color.white);
+		plot.setRangeGridlinePaint(Color.black);
+		plot.setDomainGridlinePaint(Color.black);
+//		ValueAxis domain = plot.getDomainAxis();
+//		domain.setMinorTickCount(0);
+
+		// Turn off Glossy 3D on bar chart
+		XYBarRenderer renderer = (XYBarRenderer) plot.getRenderer();
+		renderer.setBarPainter(new StandardXYBarPainter());
+
+		// Code to turn off shadows if 3D
+		// renderer.setShadowVisible(false);
+
+		// Code to set y-axis range color
+		// final IntervalMarker target = new IntervalMarker(400.0, 700.0);
+		// target.setLabelFont(new Font("SansSerif", Font.ITALIC, 11));
+		// target.setLabelAnchor(RectangleAnchor.LEFT);
+		// target.setLabelTextAnchor(TextAnchor.CENTER_LEFT);
+		// target.setPaint(new Color(222, 222, 255, 128));
+		// plot.addRangeMarker(target, Layer.BACKGROUND);
+
+		return chart;
+	}
 }

src/main/java/scriptmanager/cli/Peak_Analysis/FRiXCalculatorCLI.java

@@ -0,0 +1,253 @@
+package scriptmanager.cli.Peak_Analysis;
+
+import picocli.CommandLine.ArgGroup;
+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 scriptmanager.util.BAMUtilities;
+import scriptmanager.util.ExtensionFileFilter;
+import scriptmanager.objects.PileupParameters;
+import scriptmanager.objects.ToolDescriptions;
+import scriptmanager.objects.Exceptions.OptionException;
+import scriptmanager.scripts.Peak_Analysis.FRiXCalculator;
+
+/**
+ * Command line interface for
+ * {@link scriptmanager.scripts.Peak_Analysis.FRiXCalculator}
+ * 
+ * @author Olivia Lang
+ */
+@Command(name = "frix", mixinStandardHelpOptions = true,
+	description = ToolDescriptions.frix_description,
+	version = "ScriptManager "+ ToolDescriptions.VERSION,
+	descriptionHeading = "%nDescription:%n%n",
+	parameterListHeading = "%nParameters:%n",
+	optionListHeading = "%nGeneral Options:%n",
+	sortOptions = false,
+	exitCodeOnInvalidInput = 1,
+	exitCodeOnExecutionException = 1)
+public class FRiXCalculatorCLI implements Callable<Integer> {
+
+	@Parameters( index = "0", description = "The BED file with reference coordinate windows to tally from.")
+	private File bedFile;
+	@Parameters( index = "1", description = "The BAM file from which we remove duplicates. Make sure its indexed!")
+	private File bamFile;
+
+	@Option(names = {"-o", "--output"}, description = "specify output basename, default is the BAM input filename without extension")
+	private File outputBasename = null;
+
+	//Aspect
+	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Aspect of Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
+	AspectType aspectType = new AspectType();
+	static class AspectType {
+		@Option(names = {"-5", "--five-prime"}, description = "pileup of 5' end of read(default)")
+		boolean fiveprime = false;
+		@Option(names = {"-3", "--three-prime"}, description = "pileup of 3' end of read")
+		boolean threeprime = false;
+		@Option(names = {"-m", "--midpoint"}, description = "pileup fragment midpoints (require PE, combined)")
+		boolean midpoint = false;
+	}
+
+	//Read
+	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect Read to output:%n\t@|fg(red) (select no more than one of these options)|@%n")
+	ReadType readType = new ReadType();
+	static class ReadType {
+		@Option(names = {"-1", "--read1"}, description = "pileup of read 1 (default)")
+		boolean read1 = false;
+		@Option(names = {"-2", "--read2"}, description = "pileup of read 2")
+		boolean read2 = false;
+		@Option(names = {"-a", "--all-reads"}, description = "pileup all reads")
+		boolean allreads = false;
+	}
+
+	@ArgGroup(validate = false, heading = "%nCalculation Options:%n")
+	CalcOptions calcOptions = new CalcOptions();
+	static class CalcOptions {
+		@Option(names = {"-s", "--shift"}, description = "set a shift in bp (default=0bp)")
+		private int shift = 0;
+		@Option(names = {"--cpu"}, description = "set number of CPUs to use (default=1)")
+		private int cpu = 1;
+	}
+
+	@ArgGroup(validate = false, heading = "%nFilter Options:%n")
+	FilterOptions filterOptions = new FilterOptions();
+	static class FilterOptions {
+		@Option(names = {"-f", "--blacklist-filter"}, description = "specify a blacklist file to filter BED by, must use with -t flag")
+		private File blacklistFilter = null;
+		@Option(names = {"-p", "--require-pe"}, description = "require proper paired ends (default=false)\nautomatically turned on with any of flags -mnx")
+		private boolean requirePE = false;
+		@Option(names = {"-n", "--min-insert"}, description = "filter by minimum insert size in bp, require PE (default=no minimum)")
+		private int MIN_INSERT = -9999;
+		@Option(names = {"-x", "--max-insert"}, description = "filter by maximum insert size in bp, require PE (default=no maximum)")
+		private int MAX_INSERT = -9999;
+	}
+
+	PileupParameters p;
+
+	/**
+	 * Runs when this subcommand is called, running script in respective script
+	 * package with user defined arguments
+	 * 
+	 * @throws IOException Invalid file or parameters
+	 */
+	@Override
+	public Integer call() throws Exception {
+		System.err.println( ">FRiXCalculatorCLI.call()" );
+		p = new PileupParameters();
+		String validate = validateInput();
+		if(!validate.equals("")){
+			System.err.println(validate);
+			System.err.println("Invalid input. Check usage using '-h' or '--help'");
+			System.exit(1);
+		}
+
+		FRiXCalculator script_obj = new FRiXCalculator(bedFile, bamFile, p, null, outputBasename.getAbsolutePath());
+		script_obj.run();
+
+		System.err.println( "Calculations complete" );
+		return(0);
+	}
+
+	private String validateInput() throws IOException {
+		String r = "";
+
+		// Set ASPECT
+		if (aspectType.fiveprime) { p.setAspect(PileupParameters.FIVE); }
+		else if (aspectType.threeprime) { p.setAspect(PileupParameters.THREE); }
+		else if  (aspectType.midpoint) { p.setAspect(PileupParameters.MIDPOINT); }
+
+		// Set READ
+		if (readType.read1) { p.setRead(PileupParameters.READ1); }
+		else if (readType.read2) { p.setRead(PileupParameters.READ2); }
+		else if (readType.allreads) { p.setRead(PileupParameters.ALLREADS); }
+
+		//check inputs exist
+		if (!bedFile.exists()) {
+			r += "(!)BED file does not exist: " + bedFile.getCanonicalPath() +  "\n";
+		}
+		if (!bamFile.exists()) {
+			r += "(!)BAM file does not exist: " + bamFile.getCanonicalPath() +  "\n";
+		}
+		if (!r.equals("")) { return(r); }
+		//check BAI exists
+		File f = new File(bamFile+".bai");
+		if (!f.exists() || f.isDirectory()) {
+			r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
+		}
+
+		//set default output filename
+		if (outputBasename==null) {
+			outputBasename = new File(ExtensionFileFilter.stripExtension(bedFile) + "_" + ExtensionFileFilter.stripExtension(bamFile) + "_FRiXscore.txt");
+		//check output filename is valid
+		} else {
+			//no check ext
+			//check directory
+			if (outputBasename.getParent()==null) {
+// 				System.err.println("default to current directory");
+			} else if(!new File(outputBasename.getParent()).exists()) {
+				r += "(!)Check output directory exists: " + outputBasename.getParent() + "\n";
+			}
+		}
+
+		//set require PE for appropriate flags
+		p.setPErequire(filterOptions.requirePE);
+		if (filterOptions.MIN_INSERT!=-9999 || filterOptions.MAX_INSERT!=-9999 || p.getAspect()==2) { p.setPErequire(true); }
+
+		//validate shift, binSize, and CPUs
+		if (calcOptions.shift<0){  r += "(!)Invalid shift! Must be non-negative, shift=" + calcOptions.shift + "\n"; }
+		if (calcOptions.cpu<1){  r += "(!)Invalid Number of CPU's! Must use at least 1, CPU=" + calcOptions.cpu + "\n"; }
+
+		//validate insert sizes
+		if (filterOptions.MIN_INSERT<0 && filterOptions.MIN_INSERT!=-9999) { r += "(!)MIN_INSERT must be a positive integer value: " + p.getMinInsert() + "\n"; }
+		if (filterOptions.MAX_INSERT<0 && filterOptions.MAX_INSERT!=-9999) { r += "(!)MAX_INSERT must be a positive integer value: " + p.getMaxInsert() + "\n"; }
+		if (filterOptions.MIN_INSERT!=-9999 && filterOptions.MAX_INSERT!=-9999 && filterOptions.MAX_INSERT<filterOptions.MIN_INSERT) {
+			r += "(!)MAX_INSERT must be larger/equal to MIN_INSERT: " + filterOptions.MIN_INSERT + "," + filterOptions.MAX_INSERT + "\n";
+		}
+
+		//Set SHIFT, BIN, CPU
+		p.setShift(calcOptions.shift);
+		p.setCPU(calcOptions.cpu);
+
+		//Set Ratio (code to standardize tags sequenced to genome size (1 tag / 1 bp))
+		if (p.getStandard() && filterOptions.blacklistFilter!=null) {
+			p.setRatio(BAMUtilities.calculateStandardizationRatio(bamFile, filterOptions.blacklistFilter, p.getRead()));
+		} else if (p.getStandard()) {
+			p.setRatio(BAMUtilities.calculateStandardizationRatio(bamFile, p.getRead()));
+		}
+
+		//Set MIN_INSERT & MAX_INSERT
+		p.setMinInsert(filterOptions.MIN_INSERT);
+		p.setMaxInsert(filterOptions.MAX_INSERT);
+
+		return(r);
+	}
+
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param BED   input BED file
+	 * @param BAM   input BAM file
+	 * @param PARAM parameters for tag pileup
+	 * @return command line to execute with formatted inputs
+	 * @throws OptionException thrown by PileupParameters if invalid param values given
+	 */
+	public static String getCLIcommand(File BED, File BAM, PileupParameters PARAM) throws OptionException {
+		String command = "java -jar $SCRIPTMANAGER peak-analysis frix";
+		command += " " + BED.getAbsolutePath();
+		command += " " + BAM.getAbsolutePath();
+
+		// Add ASPECT
+		switch (PARAM.getAspect()) {
+			case PileupParameters.FIVE:
+				command += " -5";
+				break;
+			case PileupParameters.THREE:
+				command += " -3";
+				break;
+			case PileupParameters.MIDPOINT:
+				command += " -m";
+				break;
+			default:
+				throw new OptionException("Unknown PileupParameters read aspect value: " + PARAM.getAspect());
+		}
+
+		// Add READ
+		switch (PARAM.getRead()) {
+			case PileupParameters.READ1:
+				command += " -1";
+				break;
+			case PileupParameters.READ2:
+				command += " -2";
+				break;
+			case PileupParameters.ALLREADS:
+				command += " -a";
+				break;
+			default:
+				throw new OptionException("Unknown PileupParameters read output value: " + PARAM.getRead());
+		}
+
+		// Add requirePE
+		command += PARAM.getPErequire() ? " -p" : "";
+		// Add MIN_INSERT
+		if (PARAM.getMinInsert() != -9999) { command += " -n " + PARAM.getMinInsert(); }
+		// Add MAX_INSERT
+		if (PARAM.getMaxInsert() != -9999) { command += " -x " + PARAM.getMaxInsert(); }
+
+		// Add SHIFT
+		command += " -s " + PARAM.getShift();
+		// Add CPU
+		command += " --cpu " + PARAM.getCPU();
+
+		// Add output
+		String NAME = PARAM.getOutputDirectory() + File.separator + PARAM.generateFileBase(BED.getName(), BAM.getName());
+		command += " -o " + NAME;
+
+		return(command);
+	}
+}

src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java

@@ -13,9 +13,11 @@
 import java.io.IOException;
 import java.io.PrintStream;
 
-import scriptmanager.util.BAMUtilities;
 import scriptmanager.objects.PileupParameters;
 import scriptmanager.objects.ToolDescriptions;
+import scriptmanager.objects.Exceptions.OptionException;
+import scriptmanager.util.BAMUtilities;
+
 import scriptmanager.scripts.Read_Analysis.TagPileup;
 
 /**
@@ -310,11 +312,20 @@ private String validateInput() throws IOException {
 		return(r);
 	}
 
-	public static String getCLIcommand(File BED, File BAM, PileupParameters PARAM) {
+	/**
+	 * Reconstruct CLI command
+	 * 
+	 * @param BED   input BED file
+	 * @param BAM   input BAM file
+	 * @param PARAM parameters for tag pileup
+	 * @return command line to execute with formatted inputs
+	 * @throws OptionException thrown by PileupParameters if invalid param values given
+	 */
+	public static String getCLIcommand(File BED, File BAM, PileupParameters PARAM) throws OptionException {
 		String command = "java -jar $SCRIPTMANAGER read-analysis tag-pileup";
-		command += " " + PARAM.getCLIOptions();
 		command += " " + BED.getAbsolutePath();
 		command += " " + BAM.getAbsolutePath();
+		command += " " + PARAM.getCLIOptions();
 		String NAME = PARAM.getOutputDirectory() + File.separator + PARAM.generateFileBase(BED.getName(), BAM.getName());
 		command += " -M " + NAME + " -o " + NAME;
 		return(command);