Mercurial > repos > pfrommolt > ngsrich

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

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author pfrommolt
date Mon, 21 Nov 2011 08:12:19 -0500
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-1:000000000000 0:89ad0a9cca52
1 package _main;
2 import java.io.FileInputStream;
3 import java.io.IOException;
4 import java.util.Properties;
5 import java.util.Scanner;
6
7 import middlewares.Misc;
8 import exceptions.FileFormatException;
9
10 /**
11 * This is the Main-class of the summarization part of the software. This class
12 * is a wrapper class. It calls the r-script "summarize_enrichment.R" which
13 * summarizes the evaluations of multiple samples.
14 *
15 * @author Peter Frommolt
16 */
17
18 public class NGSrichSummarize {
19
20 /**
21 * An array of arguments containing the following option elements in the
22 * very same order: -i <inputIndex> -o <outDir> [-p <poor> -h <high>]
23 *
24 * Required:
25 * <inputIndex> File with evaluation directories to be summarized, one per
26 * line.
27 * <outDir> Output directory.
28 *
29 * Optional:
30 * <poor> Cutoff for poorly covered genes [default: 2].
31 * <high> Cutoff for highly covered genes [default: 200].
32 *
33 */
34 String[] args;
35
36 public NGSrichSummarize(String[] args){
37 this.args = args;
38 }
39
40 public void summarize() throws FileFormatException,
41 IOException,
42 InterruptedException{
43 int alen = args.length;
44 String[] params = new String[4];
45
46 String usagestr="\nUsage: NGSrich summarize -i <inputIndex> -o <outDir> " +
47 "[-p <poor> -h <high>]\n\n\tRequired:\n\t<inputIndex>\tFile " +
48 "with evaluation directories to be summarized, one per line." +
49 "\n\t<outDir>\tOutput directory.\n\n\tOptional:\n\t<poor>\t\t" +
50 "Cutoff for poorly covered genes [default: 2].\n\t<high>\t\t" +
51 "Cutoff for highly covered genes [default: 200].\n";
52
53 if(alen==0){
54 System.out.println(usagestr);
55 System.exit(0);
56 }
57
58 boolean i=false, o=false, h=false, po=false;
59 for(int k = 0; k < alen; k=k+2){
60 if(args[k].length() == 2 && args[k].charAt(0)=='-'){
61 char flag = args[k].charAt(1);
62 switch(flag){
63 case 'i': params[0]=args[k+1]; i=true; break;
64 case 'o': params[1]=args[k+1]; o=true; break;
65 case 'p': params[2]=args[k+1]; po=true; break;
66 case 'h': params[3]=args[k+1]; h=true; break;
67 }
68 }
69 else{
70 System.out.println(usagestr);
71 System.exit(0);
72 }
73 }
74
75 Properties p = new Properties();
76 FileInputStream stream=new FileInputStream(Misc.binDir()+Misc.slash(Misc.binDir())+"DEFAULT.properties");
77 p.load(stream); stream.close();
78
79 String infile, outdir, poor, high;
80
81 if(!i){System.out.println("Error: Argument -i is mandatory"); System.exit(1);}
82 if(!o){System.out.println("Error: Argument -o is mandatory"); System.exit(1);}
83 infile=params[0]; outdir=params[1];
84
85 if(!po){poor=p.getProperty("poor");}
86 else{poor=params[2];}
87
88 if(!h){high=p.getProperty("high");}
89 else{high=params[3];}
90
91 Runtime rt=Runtime.getRuntime();
92 String rScriptAbsolutePathName=Misc.binDir()+Misc.slash(Misc.binDir())+"../R/summarize_enrichment.R";
93 Process proc = rt.exec(rScriptAbsolutePathName+" "+infile+" "+outdir+" "+poor+" "+high);
94
95 /*Scanner sc=new Scanner(proc.getInputStream()); String erg = "";
96 while(sc.hasNextLine()){erg += (sc.nextLine());}
97 sc.close();*/
98
99 Scanner stdout = new Scanner(proc.getInputStream());
100 Scanner stderr=new Scanner(proc.getErrorStream());
101 while (stdout.hasNextLine()){System.out.println(stdout.nextLine());}
102 while(stderr.hasNextLine()){System.out.println(stderr.nextLine());}
103 stdout.close(); stderr.close();
104
105 }
106 }