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1 package converters;
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2
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3 import java.io.File;
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4 import java.io.FileNotFoundException;
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5 import java.io.FileWriter;
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6 import java.io.IOException;
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7 import java.util.Scanner;
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8
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9 import datastructures.GenomeFrame;
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10 import datastructures.ReadFrame;
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11 import datastructures.ReducedReadLine;
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12 import exceptions.ChromosomeFormatException;
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13 import exceptions.ChromosomeNotFoundException;
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14 import exceptions.RangeFormatException;
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15 import exceptions.RangeLimitNotFoundException;
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16
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17 import middlewares.Misc;
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18
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19 /**
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20 * <P>This is a converter class, wich convert a reduced alignment file with the
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21 * following format:</P>
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22 * <TABLE>
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23 * <TR>
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24 * <TD width= "140"><B>read-name</B></TD>
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25 * <TD width= "200"><B>chromosom-name</B></TD>
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26 * <TD width= "150"><B>start-position</B></TD>
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27 * <TD width= "200"><B>end-position</B></TD>
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28 * </TR>
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29 * <TR height=""></TR>
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30 * </TABLE>
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31 * <P>to the wiggle-format. The wiggle format (WIG) allows the display of continuous-
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32 * valued data in a track format and it is used to visualize the read enrichment
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33 * with the <a href="http://genome.ucsc.edu/cgi-bin/hgGateway" target="_new">ucsc genome browser</a>. Click on the following link:
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34 * <a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html" target="_new">
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35 * http://genome.ucsc.edu/goldenPath/help/wiggle.html</a> for more information.</P>
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36 *
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37 * @author Ali Abdallah
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38 * @version 06.01.2011
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39 * @since jdk 1.6.0
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40 */
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41
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42 public class Read2Wig {
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43
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44 private static final int LENGTH = 1024;
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45 private File alignFile;
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46 private File outputFile;
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47 private String outputDir;
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48 private int gMin = Integer.MAX_VALUE;
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49 private int gMax = Integer.MIN_VALUE;
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50 private FileWriter tmpWigWriter;
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51
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52 /**
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53 * Constructs and initialzes a new Read2Wig object.
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54 * Converts the read alignment file to a overall covrage wig file.
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55 *
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56 * @param alignFileName the name of the alignment file.
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57 * @throws IOException
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58 */
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59 public Read2Wig(String alignFileName,String outPrefix,String outputDir,String genome,String tmpDir) throws IOException{
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60 // Das File-Objekt zur Behandlung der Alignment-Datei erzeugen.
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61 this.alignFile = new File(alignFileName);
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62 this.outputDir = outputDir+Misc.slash(outputDir);
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63 tmpWigWriter = new FileWriter(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig");
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64 convert(alignFileName,this.outputDir,outPrefix);
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65 try{
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66 wigToBigWig("hg19",tmpDir);
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67 }
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68 catch(Exception e){
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69 System.err.println("Converting wig file to a bigwig file failed. " +
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70 "Check whether you have a 64-bit linux system!");
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71 }
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72 }
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73
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74 private void convert(String alignFileName, String outputDir,String outPrefix) throws FileNotFoundException, IOException {
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75 Scanner s = new Scanner(this.alignFile);
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76 computeExtremas(s); s.close();
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77 Scanner readScanner = new Scanner(this.alignFile);
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78 alignFileName = Misc.prefix(alignFileName);
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79 Scanner as = new Scanner(alignFileName);
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80 as.useDelimiter("_");
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81 as.next();
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82 outputFile = new File(outputDir+outPrefix+".wig");
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83 FileWriter fw = new FileWriter(outputFile);
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84
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85 annotationHeader(fw);
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86
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87 ReadFrame readF = computeNextRead(readScanner); //Current read frame
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88 GenomeFrame frame = new GenomeFrame(readF.start(), LENGTH); //Current base frame
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89 String chrom = readF.chrom(); //Current chromosome
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90 if(frame.contains(readF)){frame.updateHits(readF);} //Sum up all hits of curr read
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91 writeHeader(fw, frame, readF); //Write header line
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92
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93 while(true){
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94 while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.contains(readF)){
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95 frame.updateHits(readF); readF = computeNextRead(readScanner);
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96 }
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97 while(readScanner.hasNextLine() && chrom.equals(readF.chrom()) && frame.overlaps(readF) && !frame.limitExceeded(readF)){
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98 frame.updateFrameFromRightEnd(readF); frame.updateHits(readF); readF = computeNextRead(readScanner);
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99 }
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100 if(!readScanner.hasNextLine()){break;}
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101 else if(!chrom.equals(readF.chrom())){
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102 frame = new GenomeFrame(readF.start(), LENGTH);
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103 writeHeader(fw, frame, readF);
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104 chrom = readF.chrom();
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105 }
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106 else if(!frame.overlaps(readF)){
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107 GenomeFrame last = frame; writeFrame(fw, last);
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108 frame = new GenomeFrame(readF.start(), LENGTH);
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109 writeFrameLeak(fw, last, frame, readF);
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110 }
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111 else if(frame.limitExceeded(readF)){
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112 writeFramePortion(fw, frame, readF.start()); frame.updateFrameFromBothEnds(readF, LENGTH);
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113 }
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114 }
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115 fw.close();
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116 tmpWigWriter.close();
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117 readScanner.close();
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118 }
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119
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120 private void wigToBigWig(String genome,String tmpDir){
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121 String scriptDir = Misc.binDir()+Misc.slash(Misc.binDir());
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122 String wig2bw = scriptDir + "../thirdparty/wigToBigWig";
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123 String fetchChromSizes = scriptDir + "fetchChromSizes";
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124
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125 try {
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126 Process p = Runtime.getRuntime().exec("sh "+fetchChromSizes+" "+genome);
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127 FileWriter fw = new FileWriter(outputDir+Misc.slash(outputDir)+genome+".chrom.sizes");
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128 Scanner s = new Scanner(p.getInputStream());
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129 while(s.hasNextLine())
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130 fw.write(s.nextLine()+"\r\n");
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131 fw.close();
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132
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133 Runtime.getRuntime().exec(wig2bw+" "+outputFile.getAbsolutePath()
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134 +" "+outputDir+Misc.slash(outputDir)+genome+".chrom.sizes "+
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135 outputDir+Misc.slash(outputDir)+
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136 Misc.prefix(outputFile.getAbsolutePath())+".bw");
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137 new File(outputDir+Misc.slash(outputDir)+genome+".chrom.sizes").delete();
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138 new File(tmpDir+Misc.slash(tmpDir)+"tmpWig.wig").delete();
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139 } catch (IOException e) {
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140 // TODO Auto-generated catch block
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141 e.printStackTrace();
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142 }
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143 }
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144
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145 private void computeExtremas(Scanner s){
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146 String chrom = "Datei falsch formatiert.";
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147 String oldChrom = null;
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148 int start = -1;
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149 int end = -1;
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150 String line = s.nextLine();
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151
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152 oldChrom = chrom(line); start = start(line); end = end(line);
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153
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154 while(s.hasNextLine()){
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155 line = s.nextLine();
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156 if(isHeader(line)){
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157 chrom = chrom(line); start = start(line); end = end(line);
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158 if(gMin > start && chrom.equals(oldChrom))
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159 gMin = start;
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160
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161 if(gMax < end && chrom.equals(oldChrom))
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162 gMax = end;
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163 }
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164 }
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165 }
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166
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167 private boolean isHeader(String line){
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168 return line.indexOf("chr")!=-1;
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169 }
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170
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171 private int start(String line){
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172 Scanner s = new Scanner(line);
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173 s.next();s.next();
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174 return s.nextInt();
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175 }
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176
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177 private int end(String line){
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178 Scanner s = new Scanner(line);
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179 s.next();s.next();s.next();
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180 return s.nextInt();
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181 }
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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 s.next();
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186 return s.next();
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187 }
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188
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189 private void writeFramePortion(FileWriter fw, GenomeFrame frame, int start2) throws IOException {
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190 for(int base = frame.start(); base < start2; base++){
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191 fw.write(frame.getHit(base)+"\r\n");
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192 tmpWigWriter.write(frame.getHit(base)+"\r\n");
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193 }
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194 }
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195
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196 private void writeFrameLeak(FileWriter fw,
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197 GenomeFrame last, GenomeFrame frame, ReadFrame read)
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198 throws IOException {
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199 if(frame.start()-last.end() > 50){
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200 writeHeader(fw, frame, read);
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201 }
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202 else{
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203 for(int i = 0; i < frame.start()-last.end()-1; i++){
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204 fw.write(0+"\r\n");
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205 tmpWigWriter.write(0+"\r\n");
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206 }
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207 }
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208 }
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209
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210 private void annotationHeader(FileWriter fw) throws IOException{
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211 String browserLines = "browser position chr1:"+gMin+"-"+gMax+"\r\n"+
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212 "browser hide all"+"\r\n"+
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213 "browser pack refGene encodeRegions"+"\r\n"+
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214 "browser full altGraph";
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215 Scanner as = new Scanner(alignFile.getName());
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216 as.useDelimiter("_");as.next();
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217 String trackLine = "track type=wiggle_0 name=\""+as.next()+"\" " +
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218 "description=\"Base read coverage\" visibility=full " +
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219 "color=0,0,0 altColor=255,0,0 priority=20 " +
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220 "autoScale=on";
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221 fw.write(browserLines+"\r\n"+trackLine+"\r\n");
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222 }
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223
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224 private void writeHeader(FileWriter fw, GenomeFrame frame, ReadFrame read)
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225 throws IOException {
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226 fw.write("fixedStep chrom="+read.chrom()
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227 +" start="+frame.start()
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228 + " step=1\r\n");
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229 tmpWigWriter.write("fixedStep chrom="+read.chrom()
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230 +" start="+frame.start()
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231 + " step=1\r\n");
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232 }
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233
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234 private void writeFrame(FileWriter fw, GenomeFrame frame) throws IOException {
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235 // TODO Auto-generated method stub
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236 for(int base = frame.start(); base <= frame.end(); base++){
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237 fw.write(frame.getHit(base)+"\r\n");
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238 tmpWigWriter.write(frame.getHit(base)+"\r\n");
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239 }
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240 }
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241
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242 private ReadFrame computeNextRead(Scanner afScanner) {
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243 ReducedReadLine rl = null;
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244 try {
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245 rl = new ReducedReadLine(afScanner.nextLine());
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246 } catch (ChromosomeFormatException e) {
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247 e.printStackTrace();
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248 } catch (ChromosomeNotFoundException e) {
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249 e.printStackTrace();
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250 } catch (RangeFormatException e) {
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251 e.printStackTrace();
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252 } catch (RangeLimitNotFoundException e) {
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253 e.printStackTrace();
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254 }
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255 return new ReadFrame(rl.name(), rl.chrom(), rl.start(), rl.end());
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256 }
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257
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258 }
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