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package driver;
import fileIO.ReadWrite;
import fileIO.TextFile;
public class TransposeTextFile {
public static void main(String[] args){
int skipLines=args.length>1 ? Integer.parseInt(args[1]) : 0;
int minChrom=1;
int maxChrom=22;
for(int i=minChrom; i<=maxChrom; i++){
if(args[0].contains("#")){
process(args[0].replace("#", ""+i), skipLines);
}else{
process(args[0], skipLines);
break;
}
}
}
public static void process(String fname, int skipLines){
TextFile tf=new TextFile(fname, false);
String[] lines=tf.toStringLines();
tf.close();
String[][] lines2=TextFile.doublesplitWhitespace(lines, true);
StringBuilder sb=new StringBuilder(4096);
int columns=lines2[skipLines].length;
for(int column=0; column<columns; column++){
String tab="";
for(int row=skipLines; row<lines.length; row++){
sb.append(tab);
sb.append(lines2[row][column]);
tab="\t";
}
sb.append("\n");
}
ReadWrite.writeString(sb, fname+".transposed");
}
}
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