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1 package _main;
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2 import java.io.FileInputStream;
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3 import java.io.IOException;
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4 import java.util.Properties;
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5 import java.util.Scanner;
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6
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7 import middlewares.Misc;
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8 import exceptions.FileFormatException;
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9
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10 /**
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11 * This is the Main-class of the summarization part of the software. This class
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12 * is a wrapper class. It calls the r-script "summarize_enrichment.R" which
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13 * summarizes the evaluations of multiple samples.
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14 *
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15 * @author Peter Frommolt
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16 */
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17
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18 public class NGSrichSummarize {
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19
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20 /**
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21 * An array of arguments containing the following option elements in the
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22 * very same order: -i <inputIndex> -o <outDir> [-p <poor> -h <high>]
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23 *
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24 * Required:
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25 * <inputIndex> File with evaluation directories to be summarized, one per
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26 * line.
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27 * <outDir> Output directory.
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28 *
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29 * Optional:
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30 * <poor> Cutoff for poorly covered genes [default: 2].
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31 * <high> Cutoff for highly covered genes [default: 200].
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32 *
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33 */
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34 String[] args;
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35
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36 public NGSrichSummarize(String[] args){
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37 this.args = args;
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38 }
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39
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40 public void summarize() throws FileFormatException,
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41 IOException,
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42 InterruptedException{
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43 int alen = args.length;
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44 String[] params = new String[4];
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45
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46 String usagestr="\nUsage: NGSrich summarize -i <inputIndex> -o <outDir> " +
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47 "[-p <poor> -h <high>]\n\n\tRequired:\n\t<inputIndex>\tFile " +
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48 "with evaluation directories to be summarized, one per line." +
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49 "\n\t<outDir>\tOutput directory.\n\n\tOptional:\n\t<poor>\t\t" +
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50 "Cutoff for poorly covered genes [default: 2].\n\t<high>\t\t" +
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51 "Cutoff for highly covered genes [default: 200].\n";
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52
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53 if(alen==0){
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54 System.out.println(usagestr);
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55 System.exit(0);
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56 }
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57
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58 boolean i=false, o=false, h=false, po=false;
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59 for(int k = 0; k < alen; k=k+2){
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60 if(args[k].length() == 2 && args[k].charAt(0)=='-'){
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61 char flag = args[k].charAt(1);
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62 switch(flag){
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63 case 'i': params[0]=args[k+1]; i=true; break;
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64 case 'o': params[1]=args[k+1]; o=true; break;
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65 case 'p': params[2]=args[k+1]; po=true; break;
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66 case 'h': params[3]=args[k+1]; h=true; break;
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67 }
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68 }
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69 else{
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70 System.out.println(usagestr);
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71 System.exit(0);
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72 }
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73 }
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74
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75 Properties p = new Properties();
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76 FileInputStream stream=new FileInputStream(Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties");
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77 p.load(stream); stream.close();
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78
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79 String infile, outdir, poor, high;
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80
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81 if(!i){System.out.println("Error: Argument -i is mandatory"); System.exit(1);}
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82 if(!o){System.out.println("Error: Argument -o is mandatory"); System.exit(1);}
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83 infile=params[0]; outdir=params[1];
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84
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85 if(!po){poor=p.getProperty("poor");}
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86 else{poor=params[2];}
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87
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88 if(!h){high=p.getProperty("high");}
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89 else{high=params[3];}
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90
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91 Runtime rt=Runtime.getRuntime();
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92 String rScriptAbsolutePathName=Misc.binDir()+Misc.slash(Misc.binDir())+"../R/summarize_enrichment.R";
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93 Process proc = rt.exec(rScriptAbsolutePathName+" "+infile+" "+outdir+" "+poor+" "+high);
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94
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95 /*Scanner sc=new Scanner(proc.getInputStream()); String erg = "";
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96 while(sc.hasNextLine()){erg += (sc.nextLine());}
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97 sc.close();*/
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98
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99 Scanner stdout = new Scanner(proc.getInputStream());
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100 Scanner stderr=new Scanner(proc.getErrorStream());
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101 while (stdout.hasNextLine()){System.out.println(stdout.nextLine());}
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102 while(stderr.hasNextLine()){System.out.println(stderr.nextLine());}
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103 stdout.close(); stderr.close();
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104
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105 }
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106 }
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