diff src/pairedendCrossPlot.java @ 0:8055f3f619a1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/pairedendCrossPlot.java	Thu Mar 10 10:34:37 2016 -0500
@@ -0,0 +1,241 @@
+package pairedendCrossPlot;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.Scanner;
+
+public class pairedendCrossPlot {
+	
+	private static File READ1 = null;
+	private static File READ2 = null;
+	private static File OUTPUT = null;
+	private static int WINDOW = 500;
+	
+	private static int[] BP = null;
+	private static int[] FOR = null;
+	private static int[] REV = null;
+	
+	private static ArrayList<String> chrName = null;
+	private static ArrayList<Integer> chrStart = null;
+	
+	private static int[] FHIST = null;
+	private static int[] RHIST = null;
+	
+	public static void main(String[] args) throws FileNotFoundException {
+		loadConfig(args); //Load configuration data
+		FHIST = new int[(WINDOW * 2) + 1]; //Initialize master histograms
+		RHIST = new int[(WINDOW * 2) + 1]; //Initialize master histograms
+		System.out.println("\n" + getTimeStamp());
+	
+		//Pass through the Read2 file once in order to identify the start and stops of all chromosomes present in file
+		System.out.println("Indexing Read 2 File...");
+		indexFile(READ2);
+		System.out.println("Indexing Complete\n" + getTimeStamp());
+	
+		//Parse read 1
+		System.out.println("\n" + getTimeStamp() + "\nParsing Read 1 File...");
+		parseRead1(READ1);
+		System.out.println("\nRead 1 Parsed\n" + getTimeStamp());
+		
+		//Output histogram
+		System.out.println("\nOutputing final histogram...");
+		outputHist(OUTPUT);
+		System.out.println("Program Complete\n" + getTimeStamp());
+		
+	}
+	
+	public static void outputHist(File out) throws FileNotFoundException {
+		PrintStream OUT = new PrintStream(out);
+		for(int x = WINDOW * -1; x <= WINDOW; x++) {
+			OUT.print("\t" + x);			
+		}
+		OUT.print("\nForward_Tags");
+		for(int x = 0; x < FHIST.length; x++) {
+			OUT.print("\t" + FHIST[x]);
+		}
+		OUT.print("\nReverse_Tags");
+		for(int x = 0; x < RHIST.length; x++) {
+			OUT.print("\t" + RHIST[x]);
+		}
+		OUT.close();
+	}
+	
+	public static void parseRead1(File input) throws FileNotFoundException {
+		Scanner scan = new Scanner(READ1);
+		String currentChrom = "";
+		int currentIndex = 0;
+		while (scan.hasNextLine()) {
+			String temp = scan.nextLine();
+			if(!temp.contains("index") && !temp.contains("#")) {
+				String[] array = temp.split("\t");
+				int POS = Integer.parseInt(array[1]);
+				int F = Integer.parseInt(array[2]);
+				int R = Integer.parseInt(array[3]);
+							
+				//Check if newline's chrom is equal to current chrom in memory, reload new chrom if unequal
+				if(!currentChrom.equals(array[0])) {
+					BP = null; //reset BP immediately
+					int newIndex = chrName.indexOf(array[0]);
+					if(newIndex >= 0) {
+						System.out.println("\nLoading: " + chrName.get(newIndex));
+						loadRead2(READ2, chrName.get(newIndex), chrStart.get(newIndex), chrStart.get(newIndex + 1));
+						currentChrom = array[0];
+						currentIndex = 0;
+						System.out.println("Loading Complete\n" + getTimeStamp());
+					}
+				}
+				if(BP != null) {
+					//Update local indexes to only upload data from local tag region defined by window
+					while(POS - WINDOW > BP[currentIndex] && currentIndex < BP.length - 1) { currentIndex++; } //Find furthest upstream index in read2
+					int currentStop = currentIndex;
+			        while(POS + WINDOW > BP[currentStop] && currentStop < BP.length - 1) { currentStop++; } //Find furthest downstream index in read2
+			        
+			        //Populate histogram based on read2 tags flanking current position
+			        int[] temp_F = new int[(WINDOW * 2) + 1];
+			        int[] temp_R = new int[(WINDOW * 2) + 1];
+			        for(int x = currentIndex; x <= currentStop; x++) {
+			        	int index = BP[x] - POS + WINDOW;
+			        	if(index >= 0 && index < temp_F.length) {
+			        		temp_F[index] += FOR[x];
+			        		temp_R[index] += REV[x];
+			        	}
+			        }
+					
+			        //Populate master histogram based on score
+			        for(int x = 0; x < temp_F.length; x++) {
+			                FHIST[x] += (temp_F[x] * F);
+			                RHIST[x] += (temp_R[x] * F);
+			        }
+			        //Reverse arrays
+			        for(int x = 0; x < FHIST.length / 2; x++) {
+			        	int tempF = temp_F[x];
+			        	int tempR = temp_R[x];
+			        	temp_F[x] = temp_F[temp_F.length - x - 1];
+			            temp_F[temp_F.length - x - 1] = tempF;
+			            temp_R[x] = temp_R[temp_R.length - x - 1];
+			            temp_R[temp_R.length - x - 1] = tempR;
+			        }
+			        for(int x = 0; x < FHIST.length; x++) {
+			                FHIST[x] += (temp_R[x] * R);
+			                RHIST[x] += (temp_F[x] * R);
+			        }
+				}
+			}	
+		}
+		scan.close();
+	}
+	
+	private static void loadRead2(File input, String currentChrom, int lineStart, int lineStop) throws FileNotFoundException {
+		BP = new int[lineStop - lineStart - 1];
+		FOR = new int[lineStop - lineStart - 1];
+		REV = new int[lineStop - lineStart - 1];
+		
+		int counter = 0;
+		Scanner scan = new Scanner(READ2);
+		while (scan.hasNextLine()) {
+			String temp = scan.nextLine();
+				if(counter > lineStart) { 
+					String[] array = temp.split("\t");
+					if(array[0].equals(currentChrom)) {
+						BP[counter - lineStart - 1] = Integer.parseInt(array[1]);
+						FOR[counter - lineStart - 1] = Integer.parseInt(array[2]);
+						REV[counter - lineStart - 1] = Integer.parseInt(array[3]);
+					}
+				}
+			counter++;
+		}
+		scan.close();
+		//System.out.println(BP.length + "\t" + FOR.length + "\t" + REV.length);
+	}
+	
+	//Index Read 2 file for faster processing of chromosomes
+	public static void indexFile(File input) throws FileNotFoundException {
+		chrName = new ArrayList<String>();
+		chrStart = new ArrayList<Integer>();
+		Scanner scan = new Scanner(input);
+		int linenumber = 0;
+		while (scan.hasNextLine()) {
+			String temp = scan.nextLine();
+			if(!temp.contains("index") && !temp.contains("#")) {
+				String[] array = temp.split("\t");
+				if(!chrName.contains(array[0])) {
+					chrName.add(array[0]);
+					chrStart.add(new Integer(linenumber));
+				}
+			}
+			linenumber++;
+		}
+		chrStart.add(new Integer(linenumber));
+		scan.close();
+	}
+	
+	public static void loadConfig(String[] command){
+		for (int i = 0; i < command.length; i++) {
+			switch (command[i].charAt((1))) {
+				case 'f':
+					READ1 = new File(command[i + 1]);
+					i++;
+					break;
+				case 'r':
+					READ2 = new File(command[i + 1]);
+					i++;
+					break;
+				case 'o':
+					OUTPUT = new File(command[i + 1]);
+					i++;
+					break;
+				case 'w':
+					WINDOW = Integer.parseInt(command[i + 1]);
+					i++;
+					break;
+			}
+		}
+		if(READ1 == null) {
+			System.out.println("No Read 1 File loaded!!!\n");
+			printUsage();
+			System.exit(0);
+		}
+		if(READ2 == null) {
+			System.out.println("No Read 2 File loaded!!!\n");
+			printUsage();
+			System.exit(0);
+		}
+		if(WINDOW < 1) {
+			System.out.println("Invalid Window Size Selected!!!\n");
+			printUsage();
+			System.exit(0);	
+		}
+						
+		if(OUTPUT == null) {
+			OUTPUT = new File(READ1.getName().split("\\.")[0] + ".out");
+		}
+				
+		System.out.println("-----------------------------------------\nCommand Line Arguments:");
+		System.out.println("Read 1 file: " + READ1);
+		System.out.println("Read 2 file: " + READ2);
+		System.out.println("Output: " + OUTPUT);
+		System.out.println("Window Size: " + WINDOW);
+	}
+		
+	public static void printUsage() {
+		System.out.println("Usage: java -jar pairedendCrossPlot.jar -f [Read1File] -r [Read2File] [Options]");
+		System.out.println("-----------------------------------------");
+		System.out.println("\nRequired Parameter:");
+		System.out.println("Read 1 File:\t\t\t-f\tRead 1 scIDX file");
+		System.out.println("Read 2 File:\t\t\t-r\tRead 1 scIDX file");
+		System.out.println("\nOptional Parameters:");
+		System.out.println("Output File Name:\t\t-o\tOutput file");
+		System.out.println("Window Size +/- Reference:\t-w\t(Default = 500)");
+	}
+	
+	private static String getTimeStamp() {
+		Date date= new Date();
+		String time = new Timestamp(date.getTime()).toString();
+		return time;
+	}
+	
+}