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package pacbio;
import java.io.File;
import java.util.Random;
import dna.AminoAcid;
import dna.ChromosomeArray;
import dna.Data;
import dna.FastaToChromArrays2;
import fileIO.ReadWrite;
import shared.Shared;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Jul 16, 2012
*
*/
public class GenerateMultiChrom {
public static void main(String[] args){
ChromosomeArray cha=null;
try {
int genomeIn=Integer.parseInt(args[0]);
Data.setGenome(genomeIn);
cha=Data.getChromosome(1);
Data.unload(1, true);
} catch (NumberFormatException e) {
//ignore
}
if(cha==null){
String inname=args[0];
cha=ChromosomeArray.read(inname, 1);
}
assert(cha!=null);
int copies=Integer.parseInt(args[1]);
int build=Integer.parseInt(args[2]);
int mincontig=-1;
int maxcontig=-1;
int buffer=-1;
if(args.length>3){
mincontig=Integer.parseInt(args[3]);
maxcontig=Integer.parseInt(args[4]);
buffer=Integer.parseInt(args[5]);
System.out.println("Multichrom will be overlayed with blocks of "+buffer+" 'N'");
}
// String pattern=ROOT_GENOME+GENOME_BUILD+"/chr"+chrom+".chromC";
File f=new File(Data.ROOT_GENOME+build);
if(!f.exists()){f.mkdirs();}
for(int i=1; i<=copies; i++){
ChromosomeArray chb=makeSynthetic(cha, i);
if(buffer>0){
addN(chb, mincontig, maxcontig, buffer);
}
ReadWrite.write(chb, Data.ROOT_GENOME+build+"/chr"+i+Data.chromExtension(), false);
}
FastaToChromArrays2.writeInfo(build, copies, Data.name, "multiple_"+Data.GENOME_BUILD, false, false);
}
private static void addN(ChromosomeArray cha, int minContig, int maxContig, int buffer){
final int spread=maxContig-minContig+1;
final Random randy=new Random(cha.chromosome);
final int lim=cha.maxIndex-Tools.max(maxContig, minContig+buffer);
int contig=0;
int nextContig=minContig+randy.nextInt(spread);
for(int i=0; i<lim; i++){
byte b=cha.get(i);
if(b=='N'){contig=0;}
else{
contig++;
if(contig>=nextContig){
contig=0;
int lim2=i+buffer;
while(i<lim2){
cha.set(i, 'N');
i++;
}
nextContig=minContig+(randy.nextInt(spread)+randy.nextInt(spread))/2;
}
}
}
}
/**
* @param cha
* @param i
* @return
*/
private static ChromosomeArray makeSynthetic(ChromosomeArray cha, int chrom) {
// assert(false) : cha.array.length+", "+cha.maxIndex;
ChromosomeArray chb=new ChromosomeArray(chrom, Shared.PLUS, cha.minIndex, cha.array.length+40);
chb.maxIndex=-1;
int dif=0;
final int MIN_DIF=-12;
final int MAX_DIF=12;
final int INDEL_PERCENT=10;
final int SUB_PERCENT=1;
final int ERROR_PERCENT=INDEL_PERCENT+SUB_PERCENT;
final int ERROR_LENGTH=3;
Random randy=new Random(chrom);
int a=cha.minIndex;
int b=chb.minIndex;
while(a<=cha.array.length){
byte c=cha.get(a);
int x=(c=='N' ? 100 : randy.nextInt(100));
if(x>=ERROR_PERCENT){ //No error
chb.set(b, c);
a++;
b++;
}else if(x>=INDEL_PERCENT){//sub
byte e=c;
while(e==c){
e=AminoAcid.numberToBase[randy.nextInt(4)];
}
chb.set(b, e);
a++;
b++;
}else{//indel
boolean ins=Tools.nextBoolean(randy);
int len=Tools.min(randy.nextInt(ERROR_LENGTH), randy.nextInt(ERROR_LENGTH), randy.nextInt(ERROR_LENGTH+1))+1;
if(ins && dif+len>MAX_DIF){
ins=false;
}else if(!ins && dif-len<MIN_DIF){
ins=true;
}
if(ins){
for(int i=0; i<len; i++){
boolean same=randy.nextFloat()<0.6f; //Additional 60% chance that inserted base will be a duplicate of an existing base
int n=randy.nextInt(4);
byte e=(same ? c : AminoAcid.numberToBase[n]);
chb.set(b, e);
b++;
dif++;
}
}else{
a+=len;
dif-=len;
}
}
}
return chb;
}
}
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