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package driver;
import java.io.File;
import java.io.PrintStream;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Oct 17, 2014
*
*/
public class RenameNcbiToTid {
public static void main(String[] args){
Timer t=new Timer();
RenameNcbiToTid x=new RenameNcbiToTid(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public RenameNcbiToTid(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Shared.capBuffers(4);
ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
ReadWrite.setZipThreads(Shared.threads());
Parser parser=new Parser();
for(int i=0; i<args.length; i++){
String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(parser.parse(arg, a, b)){
//do nothing
}else if(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ReadWrite.verbose=verbose;
}else if(parser.in1==null && i==0 && Tools.looksLikeInputStream(arg)){
parser.in1=arg;
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
overwrite=parser.overwrite;
append=parser.append;
in1=parser.in1;
out1=parser.out1;
}
if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
if(!Tools.testOutputFiles(overwrite, append, false, out1)){
outstream.println((out1==null)+", "+out1);
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
}
ffout1=FileFormat.testOutput(out1, FileFormat.TEXT, null, true, overwrite, append, false);
ffin1=FileFormat.testInput(in1, FileFormat.TEXT, null, true, true);
}
void process(Timer t){
final TextFile tf;
{
tf=new TextFile(ffin1);
if(verbose){outstream.println("Started tf");}
}
final TextStreamWriter tsw;
{
tsw=new TextStreamWriter(ffout1);
tsw.start();
if(verbose){outstream.println("Started tsw");}
}
long linesProcessed=0;
long charsProcessed=0;
{
String line;
while((maxReads<0 || linesProcessed<maxReads) && (line=tf.nextLine())!=null){
linesProcessed++;
charsProcessed+=line.length();
String result=processLine(line);
if(tsw!=null && result!=null){tsw.println(result);}
}
}
errorState|=tsw.poisonAndWait();
errorState|=tf.close();
t.stop();
outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, charsProcessed, 8));
if(errorState){
throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
private static String processLine(String line){
if(line.startsWith(">ncbi")){
line=line.replaceFirst(">ncbi", ">tid");
int firstSpace=line.indexOf(' ');
line=line.substring(0, firstSpace)+"|"+line.substring(firstSpace+1);
}
return line;
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private String in1=null;
private String out1=null;
/*--------------------------------------------------------------*/
private long maxReads=-1;
/*--------------------------------------------------------------*/
private final FileFormat ffin1;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private PrintStream outstream=System.err;
public static boolean verbose=false;
public boolean errorState=false;
private boolean overwrite=true;
private boolean append=false;
}
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