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package dna;
import java.io.File;
import java.util.ArrayList;
import fileIO.TextStreamWriter;
import shared.PreParser;
import shared.Timer;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Jul 26, 2012
*
*/
public class ChromToFasta {
public static void main(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
Timer t=new Timer();
if(args[0].contains("=") && (args[0].startsWith("build") || args[0].startsWith("genome"))){
int build=Integer.parseInt(args[0].split("=")[1]);
// Data.setGenome(build);
// String s="", comma="";
// for(int i=1; i<Data.numChroms; i++){
// s=s+comma+Data.chromFname(i, build);
// comma=",";
// }
// args[0]=s;
args[0]=Data.chromFname(1, build);
args[0]=args[0].substring(0, args[0].lastIndexOf('/'));
}
String[] chromfiles=args[0].split(",");
if(chromfiles.length==1){
File f=new File(chromfiles[0]);
if(f.isDirectory()){
ArrayList<String> list=new ArrayList<String>(4);
for(File f2 : f.listFiles()){
if(!f2.isDirectory() && f2.isFile()){
String s=f2.getAbsolutePath();
if(s.endsWith(".chrom") || s.endsWith(".chromC") || s.contains(".chrom.") || s.contains(".chromC.")){
list.add(s);
}
}
}
chromfiles=list.toArray(new String[list.size()]);
}
}
String outfile=args[1];
int blocklen=Integer.parseInt(args[2]);
int trigger=(args.length>3 ? Integer.parseInt(args[3]) : 0);
TextStreamWriter tsw=new TextStreamWriter(outfile, true, false, false);
tsw.start();
if(trigger<=0){ //Write normally
for(int i=0; i<chromfiles.length; i++){
ChromosomeArray cha=ChromosomeArray.read(chromfiles[i]);
writeChrom(cha, tsw, blocklen);
}
}else{ //Break into contigs
int contig=1;
for(int i=0; i<chromfiles.length; i++){
ChromosomeArray cha=ChromosomeArray.read(chromfiles[i]);
contig=writeContigs(cha, contig, trigger, blocklen, tsw);
}
}
tsw.poison();
try {tsw.join();}
catch (InterruptedException e) {e.printStackTrace();}
t.stop();
System.err.println("Time:\t"+t);
}
public static int writeContigs(ChromosomeArray cha, int contig, int trigger, int fastaBlocklen, TextStreamWriter tsw){
StringBuilder sb=new StringBuilder(4000);
int ns=0;
for(int aloc=cha.minIndex; aloc<=cha.maxIndex; aloc++){
byte b=cha.get(aloc);
if(b=='N'){
ns++;
if(sb.length()>0){
sb.append('N');
if(ns==trigger){
sb.setLength(sb.length()-ns);
tsw.print(">"+contig+"\n");
contig++;
writeContig(sb, tsw, fastaBlocklen);
sb.setLength(0);
}
}
}else{
sb.append((char)b);
ns=0;
}
}
if(sb.length()>0){
sb.setLength(sb.length()-ns);
tsw.print(">"+contig+"\n");
contig++;
writeContig(sb, tsw, fastaBlocklen);
sb.setLength(0);
}
return contig;
}
public static void writeContig(StringBuilder sb, TextStreamWriter tsw, int blocklen){
for(int i=0; i<sb.length(); i+=blocklen){
int max=Tools.min(i+blocklen, sb.length());
tsw.println(sb.substring(i, max));
}
}
public static void writeChrom(ChromosomeArray cha, String fname, int blocklen){
TextStreamWriter tsw=new TextStreamWriter(fname, true, false, false);
tsw.start();
tsw.print(">"+cha.chromosome+"\n");
writeChrom(cha, tsw, blocklen);
tsw.poison();
}
public static void writeChrom(ChromosomeArray cha, TextStreamWriter tsw, int blocklen){
tsw.println(">"+cha.chromosome);
for(int i=0; i<=cha.maxIndex; i+=blocklen){
int max=Tools.min(i+blocklen-1, cha.maxIndex);
tsw.println(cha.getString(i, max));
}
}
}
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