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package align2;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import dna.ChromosomeArray;
import dna.Data;
import dna.FastaToChromArrays2;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.SummaryFile;
import shared.Shared;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Sep 25, 2013
*
*/
public class RefToIndex {
public static final void clear(){
chromlist=null;
}
public static String summaryLoc(int build){
String s=IndexMaker4.fname(1, 1, 13, 1, build);
String dir=new File(s).getParent();
dir=dir.replace('\\', '/');
dir=dir.replace("ref/index/", "ref/genome/");
String sf=dir+"/summary.txt";
return sf;
}
public static String bloomLoc(int build){
return Data.ROOT_INDEX+build+"/bloom.serial";
}
public static void makeIndex(String reference, int build, PrintStream sysout, int keylen){
assert(reference!=null);
{
File f=new File(reference);
if(!f.exists() || !f.isFile() || !f.canRead()){
if(!reference.startsWith("stdin")){
throw new RuntimeException("Cannot read file "+f.getAbsolutePath());
}
}else{
FileFormat ff=FileFormat.testInput(reference, FileFormat.FA, null, false, true, true);
if(!ff.fasta()){
throw new RuntimeException("Reference file is not in fasta format: "+reference+"\n"+ff);
}
}
}
String s=IndexMaker4.fname(1, 1, keylen, 1);
String dir=new File(s).getParent();
dir=dir.replace('\\', '/');
final String base=dir.substring(0, dir.length()-7);
final String args=(Shared.COMMAND_LINE==null ? "null" : Arrays.toString(Shared.COMMAND_LINE));
final String indexlog=base+"build"+build+"_"+
(System.nanoTime()&Long.MAX_VALUE)+"."+((args==null ? (reference==null ? "null" : reference) : args).hashCode()&Integer.MAX_VALUE)+".log";
dir=dir.replace("ref/index/", "ref/genome/");
String sf=dir+"/summary.txt";
if(FORCE_READ_ONLY || (!NODISK && new File(sf).exists() && SummaryFile.compare(sf, reference))){
//do nothing
if(LOG && !NODISK){
if(!new File(base).exists()){new File(base).mkdirs();}
ReadWrite.writeString(new Date()+"\nFound an already-written genome for build "+build+".\n"+args+"\n", indexlog, true);
}
sysout.println("NOTE:\tIgnoring reference file because it already appears to have been processed.");
sysout.println("NOTE:\tIf you wish to regenerate the index, please manually delete "+dir+"/summary.txt");
}else{
if(NODISK){}
else{//Delete old data if present
File f=new File(dir);
if(f.exists()){
File[] f2=f.listFiles();
if(f2!=null && f2.length>0){
if(overwrite || f2[0].getAbsolutePath().equals(new File(reference).getAbsolutePath())){
sysout.println("NOTE:\tDeleting contents of "+dir+" because reference is specified and overwrite="+overwrite);
if(LOG && !NODISK){ReadWrite.writeString(new Date()+"\nDeleting genome for build "+build+".\n"+args+"\n", indexlog, true);}
for(File f3 : f2){
if(f3.isFile()){
String f3n=f3.getName();
if((f3n.contains(".chrom") || f3n.endsWith(".txt") || f3n.endsWith(".txt.gz")) && !f3n.endsWith("list.txt")){
f3.delete();
}
}
}
}else{
sysout.println(Arrays.toString(f2));
if(LOG && !NODISK){ReadWrite.writeString(new Date()+"\nFailed to overwrite genome for build "+build+".\n"+args+"\n", indexlog, true);}
throw new RuntimeException("\nThere is already a reference at location '"+f.getAbsolutePath()+"'. " +
"Please delete it (and the associated index), or use a different build ID, " +
"or remove the 'reference=' parameter from the command line, or set overwrite=true.");
}
}
}
dir=dir.replace("ref/genome/", "ref/index/");
f=new File(dir);
if(f.exists()){
File[] f2=f.listFiles();
if(f2!=null && f2.length>0){
if(overwrite){
sysout.println("NOTE:\tDeleting contents of "+dir+" because reference is specified and overwrite="+overwrite);
if(LOG && !NODISK){ReadWrite.writeString(new Date()+"\nDeleting index for build "+build+".\n"+args+"\n", indexlog, true);}
for(File f3 : f2){
if(f3.isFile()){f3.delete();}
}
}else{
if(LOG && !NODISK){ReadWrite.writeString(new Date()+"\nFailed to overwrite index for build "+build+".\n"+args+"\n", indexlog, true);}
throw new RuntimeException("\nThere is already an index at location '"+f.getAbsolutePath()+"'. " +
"Please delete it, or use a different build ID, or remove the 'reference=' parameter from the command line.");
}
}
}
}
if(!NODISK){
sysout.println("Writing reference.");
if(LOG && !NODISK){
if(!new File(base).exists()){new File(base).mkdirs();}
ReadWrite.writeString(new Date()+"\nWriting genome for build "+build+".\n"+args+"\n", indexlog, true);
}
}
int oldzl=ReadWrite.ZIPLEVEL;
ReadWrite.ZIPLEVEL=Tools.max(4, ReadWrite.ZIPLEVEL);
//assert(false) : "minScaf="+minScaf+", midPad="+midPad+", maxChromLen="+maxChromLen+
// ", startPad="+startPad+", stopPad="+stopPad+", FastaToChromArrays2.END_PADDING="+FastaToChromArrays2.END_PADDING;
maxChromLen=maxChromLen>0 ? maxChromLen : AUTO_CHROMBITS ? FastaToChromArrays2.MAX_LENGTH : ((1L<<(31-(chrombits<0 ? 2 : chrombits)))-200000);
minScaf=minScaf>-1 ? minScaf : FastaToChromArrays2.MIN_SCAFFOLD;
midPad=midPad>-1 ? midPad : FastaToChromArrays2.MID_PADDING;
startPad=startPad>-1 ? startPad : FastaToChromArrays2.START_PADDING;
stopPad=stopPad>-1 ? stopPad : FastaToChromArrays2.END_PADDING;
String[] ftcaArgs=new String[] {reference, ""+build, "writeinthread=false", "genscaffoldinfo="+genScaffoldInfo, "retain", "waitforwriting=false",
"gz="+(Data.CHROMGZ), "maxlen="+maxChromLen,
"writechroms="+(!NODISK), "minscaf="+minScaf, "midpad="+midPad, "startpad="+startPad, "stoppad="+stopPad, "nodisk="+NODISK};
chromlist=FastaToChromArrays2.main2(ftcaArgs);
ReadWrite.ZIPLEVEL=oldzl;
}
}
public static boolean AUTO_CHROMBITS=true;
public static boolean LOG=false;
public static boolean NODISK=false;
public static boolean FORCE_READ_ONLY=false;
public static boolean overwrite=true;
public static boolean append=false;
public static boolean genScaffoldInfo=true;
public static long maxChromLen=-1;
public static int minScaf=-1, midPad=-1, stopPad=-1, startPad=-1;
public static int chrombits=-1;
// public static int minScaf=FastaToChromArrays2.MIN_SCAFFOLD;
// public static int midPad=FastaToChromArrays2.MID_PADDING;
// public static int startPad=FastaToChromArrays2.START_PADDING;
// public static int stopPad=FastaToChromArrays2.END_PADDING;
public static ArrayList<ChromosomeArray> chromlist=null;
}
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