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package driver;
import fileIO.TextFile;
/**
* @author Brian Bushnell
* @date Oct 10, 2013
*
*/
public class CollateSpikeIn {
public static void main(String[] args){
// Executing align2.BBMapPacBio [minratio=0.40, fastareadlen=500, out=null, in=/projectb/shared/pacbio/jobs/026/026437/data/filtered_subreads.fasta]
System.out.println("jobID\t%Control (BBMap)\t%Accuracy (BBMap)");
TextFile tf=new TextFile(args[0], false);
String file=null, mapped=null, acc=null;
String line=tf.nextLine();
while(line!=null){
if(line.startsWith("mapped:")){
String[] split=line.split("\\p{javaWhitespace}+");
mapped=split[1].replace("%", "");
}else if(line.startsWith("Match Rate:")){
String[] split=line.split("\\p{javaWhitespace}+");
acc=split[2].replace("%", "");
System.out.println(file+"\t"+mapped+"\t"+acc);
file=acc=mapped=null;
}else if(line.startsWith("Executing align2.BBMap")){
String[] split=line.split("\\p{javaWhitespace}+");
for(String s : split){
if(s.startsWith("in=")){
file=s.replace("in=", "").replace("]", "").replace(",", "");
file=file.replace("/projectb/shared/pacbio/jobs/", "").replace("/data/filtered_subreads.fasta", "");
file=file.substring(file.indexOf('/')+1);
mapped=acc=null;
break;
}
}
}
line=tf.nextLine();
}
}
}
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