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package jgi;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
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 3, 2014
*
*/
public class PhylipToFasta {
public static void main(String[] args){
Timer t=new Timer();
PhylipToFasta x=new PhylipToFasta(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public PhylipToFasta(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
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 if(parser.out1==null && i==1 && !arg.contains("=")){
parser.out1=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();
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.FASTA, null, true, overwrite, append, false);
ffin1=FileFormat.testInput(in1, FileFormat.PHYLIP, ".phylip", true, true);
}
void process(Timer t){
ArrayList<StringBuilder> data=new ArrayList<StringBuilder>();
long bases=0;
{
final TextFile tf=new TextFile(ffin1);
String s=tf.nextLine(); //first line is some numbers
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(s.startsWith(" ")){break;}
StringBuilder sb=new StringBuilder();
data.add(sb);
sb.append('>');
int pos=0;
for(pos=0; pos<s.length(); pos++){
char c=s.charAt(pos);
if(Character.isWhitespace(c)){break;}
sb.append(c);
}
sb.append('\n');
while(pos<s.length() && Character.isWhitespace(s.charAt(pos))){pos++;}
while(pos<s.length()){
char c=s.charAt(pos);
if(Character.isLetter(c)){
sb.append(c);
bases++;
}
pos++;
}
}
final int mod=data.size();
for(int i=0; s!=null; i++){
StringBuilder sb=data.get(i%mod);
for(int pos=0; pos<s.length(); pos++){
char c=s.charAt(pos);
if(Character.isLetter(c)){
sb.append(c);
bases++;
}
pos++;
}
s=tf.nextLine();
}
errorState|=tf.errorState;
}
final long reads=data.size();
if(ffout1!=null){
TextStreamWriter tsw=new TextStreamWriter(ffout1);
tsw.start();
for(int i=0; i<data.size(); i++){
StringBuilder sb=data.set(i, null);
sb.append('\n');
tsw.print(sb);
}
tsw.poisonAndWait();
errorState|=tsw.errorState;
}
t.stop();
outstream.println(Tools.timeReadsBasesProcessed(t, reads, bases, 8));
if(errorState){
throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private String in1=null;
private String out1=null;
/*--------------------------------------------------------------*/
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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