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