comparison NGSrich_0.5.5/src/_main/NGSrichEvaluate.java @ 0:89ad0a9cca52 default tip

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0:89ad0a9cca52

package _main;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.sql.Time;
import java.util.Properties;
import middlewares.Misc;
import exceptions.ChromosomeMismatchException;
import exceptions.FileFormatException;

/**
 * This is the Main-class of the evaluation part of the software. This class
 * uses the Enrichment-class to process the phases (the parts) of the pipeline.
 * 
 * @author Ali Abdallah
 */

public class NGSrichEvaluate {

	/**
	 * An array of arguments containing the following option elements in the 
	 * following order:
	 * -r <readsFile> (-a|-g) <annotation> -t <target> [-s <sName>] 
	 * [-T <tmpDir>][-o <outDir>][-p <poor> -h <high>][-no_details]
	 * 
	 * Required:
	 * <readsFile> 	Path to read alignment file in SAM or BAM format.
	 * <annotation> UCSC genome version name.
	 * <target>		Path to target file in BED format.
	 * 
	 * Optional:
	 * <sName> 		Sample name [default: prefix of <readsFile>].
	 * <tmpDir> 	Temporary directory [default: '/tmp'].
	 * <outDir> 	Output directory [default: '<pathToReadsFile>/enrichment'].
	 * <poor> 		Cutoff for poor coverage [default: 2].
	 * <high> 		Cutoff for high coverage [default: 200].
	 */
	String[] args;

	public NGSrichEvaluate(String[] args) {
		this.args = args;
	}

	public void evaluate() throws IOException, FileFormatException,
			InterruptedException {
		/**
		 * Ordered List of Parameter (left/right): readFName genomeFName
		 * targetFName tmpDir outDir
		 * 
		 */

		int alen = args.length;
		String[] params = new String[10];

		String usagestr = 
				"\nUsage: java NGSrich evaluate -r <readsFile> " 
				+ "-u <genome-name> -t <target> [(-a|-g) "
				+ "<annotation>] [-s <sName>] [-T <tmpDir>] "
				+ "[-o <outDir>] [-p <poor> -h <high>][--no-details>]\n\n\tRequired:\n\t"
				+ "<readsFile>\tPath to read alignment file in SAM or BAM format."
				+ "\n\t<genome-name>\tUCSC genome version name.\n\t<target>\tPath "
				+ "to target file in BED format.\n\n\tOptional:\n\t<sName>\t\t"
				+ "Sample name [default: prefix of <readsFile>].\n\t<annotation>\t\t"
				+ "path of the annotation file [default: the genome is " 
				+ "downloaded based on the genome version name].\n\t<tmpDir>\t"
				+ "Temporary directory [default: '/tmp'].\n\t<outDir>\tOutput "
				+ "directory [default: '<pathToReadsFile>/enrichment'].\n\t"
				+ "<poor>\t\tCutoff for poor coverage [default: 2].\n\t<high>"
				+ "\t\tCutoff for high coverage [default: 200]. \n\t--no-details\tto repress the computation of the" +
						" evaluation details\n";
		
		if (alen == 0) {
			System.out.println(usagestr);
			System.exit(0);
		}

		boolean t = false, o = false, h = false, po = false, sname = false, u = false, r = false, g = false,
				a = false, T = false;
		params[9] = "1";
		for (int i = 0; i < alen; i = i + 2) {
			if ((args[i].length() == 2 && args[i].charAt(0) == '-') || args[i].equals("--no-details")) {
				char flag = (args[i].length()==2)?args[i].charAt(1):args[i].charAt(2);
				switch (flag) {
				case 'r': params[0] = args[i + 1];r = true;break;
				case 'g': params[1] = args[i + 1];g = true;break;
				case 'a': params[1] = args[i + 1];a = true;break;
				case 't': params[2] = args[i + 1];t = true;break;
				case 'T': params[3] = args[i + 1];T = true;break;
				case 'o': params[4] = args[i + 1];o = true;break;
				case 'p': params[5] = args[i + 1];po = true;break;
				case 'h': params[6] = args[i + 1];h = true;break;
				// Added by PF 2011-07-12
				case 's': params[7] = args[i + 1];sname = true;break;
				case 'u': params[8] = args[i+1]; u = true;break;
				case 'n': params[9]="0";break;
				}
			} else {
				System.out.println(usagestr);
				System.exit(0);
			}
		}
		
		boolean required = r && t && u;
		
		if(!required){
			System.out.println("Some required arguments are missing.\n");
			System.out.println(usagestr);
			System.exit(0);
		}

		String default_properties_file = createDefaultPropertiesFile();
		Properties p = new Properties();
		BufferedInputStream stream = 
					new BufferedInputStream(
						new FileInputStream(default_properties_file));

		p.load(stream);
		stream.close();
		if (!T)params[3] = p.getProperty("tmpDir");
		if (!o) {
			String oPath = p.getProperty("outDirPath");
			if (oPath.equals(""))oPath = Misc.path(params[0]);
			params[4] = oPath + Misc.slash(oPath) + p.getProperty("outDir");
			new File(params[4]).mkdir();
		}
		if (!po)params[5] = p.getProperty("poor");
		if (!h)params[6] = p.getProperty("high");
		if (!sname)params[7] = "none";
		if (!(a||g))params[1] = "none";
		
		Enrichment ngs = new Enrichment(params);
		// Convert BAM to SAM if necessary.
		String infile = params[0];
		if (infile.endsWith(".bam")) {
			System.out.println("======================0======================");
			System.out.println("\n>>> Found BAM file: converting to SAM\n");
			infile = ngs.bam2sam();
		}
		ngs.readFileName = infile;

		//		File timeReport = 
		//	new File(params[3] + Misc.slash(params[3])+"TimeReport.txt");
		//		FileWriter trWriter = new FileWriter(timeReport);
		
		// Reduce the files.
		System.out.println("======================1======================");
		System.out.println(">>> STEP 1: reducing files\n");
		try {
			long start = System.currentTimeMillis();
			ngs.reduceFiles();
			long rtime = System.currentTimeMillis() - start;
			Time time = new Time(rtime);
			//trWriter.write("Reducing files took: " + time + "\n");

		} catch (ChromosomeMismatchException e) {
			e.printStackTrace();
		}
		
		// Compute the target coverage files.
		System.out.println("\n======================2======================");
		System.out.println(">>> STEP 2: computing target coverage data\n");
		long start = System.currentTimeMillis();
		ngs.computeTargetCoverageFiles();
		long rtime = System.currentTimeMillis() - start;
		Time time = new Time(rtime);
		//		trWriter.write("Computing target coverage data took: " + time + "\n");
		
		// Evaluate enrichment.
		System.out.println("\n======================3======================");
		System.out.println(">>> STEP 3: evaluating enrichment files\n");
		start = System.currentTimeMillis();
		ngs.evaluate();
		rtime = System.currentTimeMillis() - start;
		time = new Time(rtime);
		//trWriter.write("Evaluating enrichment files took: " + time + "\n");
		Thread.sleep(10000);
		
		// Compute the target wiggle files.
		System.out.println("\n======================4======================");
		System.out.println(">>> STEP 4: computing targets wiggle data\n");
		start = System.currentTimeMillis();
		ngs.computeWiggleFile();
		rtime = System.currentTimeMillis() - start;
		time = new Time(rtime);
		//trWriter.write("Computing targets wiggle data took: " + time + "\n");

		// Compute the overall wiggle files.
		System.out.println("\n======================5======================");
		System.out.println(">>> STEP 5: computing overall wiggle data\n");
		ngs.computeOverallWiggleFile();
		start = System.currentTimeMillis();
		ngs.computeOverallWiggleFile();
		rtime = System.currentTimeMillis() - start;
		time = new Time(rtime);
		//trWriter.write("Computing targets wiggle data took: " + time + "\n");
		System.out.println("\n=============================================");
		//trWriter.close();
	}

	private String createDefaultPropertiesFile() throws IOException {
		String default_properties_file = 
			Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties";
		if(!new File(default_properties_file).exists()){
			String default_str = 
				"! Path of the temporary directory.\n" +
				"tmpDir: /tmp\n" +
				"! Path of the father directory of the output directory. " +
				"When empty the output directory is placed in the directory " +
				"containing the reads alignment file.\n" +
				"outDirPath:\n" +
				"! Name of the output directory (not the path).\n" +
				"outDir: enrichment\n" +
				"! Define poorly covered genes.\n" +
				"poor: 2\n" +
				"! Defines highly covered genes.\n" +
				"high: 200";
			FileWriter properties_writer = 
									new FileWriter(default_properties_file);
			properties_writer.write(default_str);
			properties_writer.close();
		}
		return default_properties_file;
	}
}