annotate NGSrich_0.5.5/src/_main/NGSrichSummarize.java @ 0:89ad0a9cca52 default tip

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package _main;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Properties;
import java.util.Scanner;

import middlewares.Misc;
import exceptions.FileFormatException;

/**
 * This is the Main-class of the summarization part of the software. This class
 * is a wrapper class. It calls the r-script "summarize_enrichment.R" which
 * summarizes the evaluations of multiple samples. 
 * 
 * @author Peter Frommolt
 */

public class NGSrichSummarize {

	/**
	 * An array of arguments containing the following option elements in the 
	 * very same order: -i <inputIndex> -o <outDir> [-p <poor> -h <high>]
	 * 
	 * Required: 
	 * <inputIndex> File with evaluation directories to be summarized, one per 
	 * 				line.
	 * <outDir> 	Output directory.
	 * 
	 * Optional:
	 * <poor> Cutoff for poorly covered genes [default: 2].
	 * <high> Cutoff for highly covered genes [default: 200].
	 * 
	 */
	String[] args;
	
	public NGSrichSummarize(String[] args){
		this.args = args;
	}

	public void summarize() throws 	FileFormatException,
									IOException, 
									InterruptedException{
		int alen = args.length;
		String[] params = new String[4];
	
		String usagestr="\nUsage: NGSrich summarize -i <inputIndex> -o <outDir> " +
				"[-p <poor> -h <high>]\n\n\tRequired:\n\t<inputIndex>\tFile " +
				"with evaluation directories to be summarized, one per line." +
				"\n\t<outDir>\tOutput directory.\n\n\tOptional:\n\t<poor>\t\t" +
				"Cutoff for poorly covered genes [default: 2].\n\t<high>\t\t" +
				"Cutoff for highly covered genes [default: 200].\n";

		if(alen==0){
		    System.out.println(usagestr);
		    System.exit(0);
		}

		boolean i=false, o=false, h=false, po=false;
		for(int k = 0; k < alen; k=k+2){
			if(args[k].length() == 2 && args[k].charAt(0)=='-'){
			    char flag = args[k].charAt(1);
			    switch(flag){
			    case 'i': params[0]=args[k+1]; i=true; break;
			    case 'o': params[1]=args[k+1]; o=true; break;
			    case 'p': params[2]=args[k+1]; po=true; break;
			    case 'h': params[3]=args[k+1]; h=true; break;
			    }
			}
			else{
			    System.out.println(usagestr);
			    System.exit(0);
			}
		}

		Properties p = new Properties();
		FileInputStream stream=new FileInputStream(Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties");
		p.load(stream); stream.close();
				
		String infile, outdir, poor, high;

		if(!i){System.out.println("Error: Argument -i is mandatory"); System.exit(1);}
		if(!o){System.out.println("Error: Argument -o is mandatory"); System.exit(1);}
		infile=params[0]; outdir=params[1];

		if(!po){poor=p.getProperty("poor");}
		else{poor=params[2];}
		
		if(!h){high=p.getProperty("high");}
		else{high=params[3];}

		Runtime rt=Runtime.getRuntime();
		String rScriptAbsolutePathName=Misc.binDir()+Misc.slash(Misc.binDir())+"../R/summarize_enrichment.R";
		Process proc = rt.exec(rScriptAbsolutePathName+" "+infile+" "+outdir+" "+poor+" "+high);
			
		/*Scanner sc=new Scanner(proc.getInputStream()); String erg = "";
		while(sc.hasNextLine()){erg += (sc.nextLine());}
		sc.close();*/

		Scanner stdout = new Scanner(proc.getInputStream());
		Scanner stderr=new Scanner(proc.getErrorStream());
		while (stdout.hasNextLine()){System.out.println(stdout.nextLine());}
		while(stderr.hasNextLine()){System.out.println(stderr.nextLine());}
		stdout.close(); stderr.close();

	}
}