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comparison NGSrich_0.5.5/src/converters/ReadOnTarget2Wig.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 converters;
2 import java.io.File;
3 import java.io.FileWriter;
4 import java.io.IOException;
5 import java.util.Scanner;
6 import middlewares.Misc;
7
8 /**
9 * Converts the detailed coverage data to the wig format. Used for the
10 * visualization of the coverage data in the ucsc-browser.
11 *
12 * @author Ali Abdallah
13 * @version 20.07.2011
14 * @since Java 1.6
15 */
16 public class ReadOnTarget2Wig {
17
18 private int
19 /**
20 * The maximal number of hits on a base.
21 */
22 max,
23 /**
24 * The minimal number of hits on a base.
25 */
26 min,
27 /**
28 * The minimal position on chr1.
29 */
30 gMin,
31 /**
32 * the maximal position on chr1.
33 */
34 gMax;
35
36 private String
37 /**
38 * The name of the file of detailed coverage data.
39 */
40 filename,
41 /**
42 * The title of the track.
43 */
44 title;
45
46 /**
47 * Constructs an new ReadOnTarget2Wig object, initializes the parameters
48 * and call the conversion method.
49 *
50 * @param filename
51 * @param prefix
52 * @param outDir
53 * @param title
54 * @throws IOException
55 */
56 public ReadOnTarget2Wig(String filename, String prefix, String outDir, String title) throws IOException{
57 this.filename = filename;
58 max = Integer.MIN_VALUE; gMax = Integer.MIN_VALUE;
59 min = Integer.MAX_VALUE; gMin = Integer.MAX_VALUE;
60 this.title = title;
61 File f=new File(this.filename);
62 FileWriter fw=new FileWriter(outDir+Misc.slash(outDir)
63 +prefix+"_onTarget.wig");
64 Scanner scanForMinMax=new Scanner(f);
65 computeExtremas(scanForMinMax);
66 scanForMinMax.close();
67
68 Scanner s = new Scanner(f);
69 annotationHeader(fw);
70 toWiggleFormat(fw,s);
71 fw.close();
72 }
73
74 /**
75 * Writes the annotation header to the wig file.
76 *
77 * @param fw FileWriter
78 * @throws IOException if write operation is not possible.
79 */
80 private void annotationHeader(FileWriter fw) throws IOException{
81 String browserLines = "browser position chr1:"+gMin+"-"+gMax+"\r\n"+
82 "browser hide all"+"\r\n"+
83 "browser pack refGene encodeRegions"+"\r\n"+
84 "browser full altGraph";
85 String trackLine = "track type=wiggle_0 name=\""+title+"\" " +
86 "description=\"Base read coverage\" visibility=full "
87 +"color=0,0,0 altColor=255,0,0 priority=20 " +
88 "autoScale=off graphType=bar " +
89 "viewLimits="+min+":"+max;
90 fw.write(browserLines+"\r\n"+trackLine+"\r\n");
91 }
92
93 /**
94 * Computes the hit and position minimas and maxima.
95 *
96 * @param s the reader of the file of detailed coverage data.
97 */
98 private void computeExtremas(Scanner s){
99 String chrom = "Datei falsch formatiert.";
100 int start = -1; int end = -1;
101 while(s.hasNextLine()){
102 String line = s.nextLine();
103 if(isHeader(line)){
104 chrom = chrom(line); start = start(line); end = end(line);
105 if(gMin > start && chrom.equals("chr1")){gMin = start;}
106 if(gMax < end && chrom.equals("chr1")){gMax = end;}
107 }
108 else{
109 if(min > Integer.parseInt(line.trim())){
110 min = Integer.parseInt(line.trim());
111 }
112 if(max < Integer.parseInt(line.trim())){
113 max = Integer.parseInt(line.trim());
114 }
115 }
116 }
117 }
118
119 /**
120 * The main computation: conversion to wiggle format.
121 *
122 * @param fw FileWriter into the wig-file.
123 * @param s the reader of the file of detailed coverage data.
124 * @throws IOException if i/o fails.
125 */
126 private void toWiggleFormat(FileWriter fw, Scanner s) throws IOException {
127 String chrom = "Datei falsch formatiert.";
128 int start = -1;
129 while(s.hasNextLine()){
130 String line = s.nextLine();
131 if(isHeader(line)){
132 chrom = chrom(line); start = start(line);
133 fw.write(declarationLine(chrom, start));
134 }
135 else fw.write(line+"\r\n");
136 }
137 }
138
139 /**
140 * @param chrom
141 * @param start
142 * @return a String representing the declaration line corresponding to the
143 * specified parameters.
144 */
145 private String declarationLine(String chrom, int start) {
146 return "fixedStep chrom="+chrom+" start="+start+" step=1\r\n";
147 }
148
149 /**
150 * Check if the specified line is a header line.
151 *
152 * @param line the current observerd line in the file of detailed coverage
153 * data.
154 * @return true if line is a header and false otherwise.
155 */
156 private boolean isHeader(String line){
157 return line.indexOf("chr")!=-1;
158 }
159
160 /**
161 * @param line
162 * @return the start position of the current frame (header).
163 */
164 private int start(String line){
165 Scanner s = new Scanner(line);
166 s.next(); return s.nextInt();
167 }
168
169 /**
170 * @param line
171 * @return the end position of the current frame.
172 */
173 private int end(String line){
174 Scanner s = new Scanner(line);
175 s.next(); s.next();
176 return s.nextInt();
177 }
178
179 /**
180 * @param line
181 * @return the chromosome corresponding to the current frame.
182 */
183 private String chrom(String line){
184 Scanner s = new Scanner(line);
185 return s.next();
186 }
187 }