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package bloom;
import java.util.ArrayList;
import dna.AminoAcid;
import fileIO.FileFormat;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.FastaReadInputStream;
import stream.Read;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Jul 5, 2012
*
*/
public class KmerCount4 extends KmerCountAbstract {
public static void main(String[] args){
Timer t=new Timer();
String fname1=args[0];
String fname2=(args.length>3 || args[1].contains(".") ? args[1] : null);
int k=14;
int cbits=16;
int gap=0;
for(int i=(fname2==null ? 1 : 2); i<args.length; i++){
final String arg=args[i];
final String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("k") || a.equals("kmer")){
k=Integer.parseInt(b);
}else if(a.startsWith("cbits") || a.startsWith("cellbits")){
cbits=Integer.parseInt(b);
}else if(a.startsWith("gap")){
gap=Integer.parseInt(b);
}else{
throw new RuntimeException("Unknown parameter "+args[i]);
}
}
KCountArray2 count=null;
if(fileIO.FileFormat.hasFastaExtension(fname1)){
assert(!FastaReadInputStream.SPLIT_READS);
FastaReadInputStream.MIN_READ_LEN=k;
}
if(gap==0){
count=count(fname1, fname2, k, cbits, true);
}else{
count=countFastqSplit(fname1, fname2, (k+1)/2, k/2, gap, cbits, true, null);
}
t.stop();
System.out.println("Finished counting; time = "+t);
printStatistics(count);
}
public static void printStatistics(KCountArray2 count){
long[] freq=count.transformToFrequency();
// System.out.println(count+"\n");
// System.out.println(Arrays.toString(freq)+"\n");
long sum=sum(freq);
System.out.println("Kmer fraction:");
int lim1=8, lim2=16;
for(int i=0; i<lim1; i++){
String prefix=i+"";
while(prefix.length()<8){prefix=prefix+" ";}
System.out.println(prefix+"\t"+Tools.format("%.3f%% ",(100l*freq[i]/(double)sum))+"\t"+freq[i]);
}
while(lim1<=freq.length){
int x=0;
for(int i=lim1; i<lim2; i++){
x+=freq[i];
}
String prefix=lim1+"-"+(lim2-1);
if(lim2>=freq.length){prefix=lim1+"+";}
while(prefix.length()<8){prefix=prefix+" ";}
System.out.println(prefix+"\t"+Tools.format("%.3f%% ",(100l*x/(double)sum))+"\t"+x);
lim1*=2;
lim2=min(lim2*2, freq.length);
}
long sum2=sum-freq[0];
long x=freq[1];
System.out.println();
System.out.println("Keys Counted: \t \t"+keysCounted);
System.out.println("Unique: \t \t"+sum2);
System.out.println("Avg Sites/Key: \t \t"+Tools.format("%.3f ",(keysCounted*1d/sum2)));
System.out.println();
System.out.println("Singleton: \t"+Tools.format("%.3f%% ",(100l*x/(double)sum2))+"\t"+x);
x=sum2-x;
System.out.println("Useful: \t"+Tools.format("%.3f%% ",(100l*x/(double)sum2))+"\t"+x);
}
public static KCountArray2 count(String reads1, String reads2, int k, int cbits, boolean rcomp){
return count(reads1, reads2, k, cbits, rcomp, null);
}
public static KCountArray2 count(String reads1, String reads2, int k, int cbits, boolean rcomp, KCountArray2 count){
assert(k>=1 && k<20);
final int kbits=2*k;
final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
if(count==null){
final long cells=1L<<kbits;
if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
count=new KCountArray2(cells, cbits);
}
final ConcurrentReadInputStream cris;
{
FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
cris.start(); //4567
}
assert(cris!=null) : reads1;
System.err.println("Started cris");
boolean paired=cris.paired();
if(verbose){System.err.println("Paired: "+paired);}
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
if(reads!=null && !reads.isEmpty()){
Read r=reads.get(0);
assert(paired==(r.mate!=null));
}
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
//System.err.println("reads.size()="+reads.size());
for(Read r : reads){
readsProcessed++;
addRead(r, count, k, mask, rcomp);
if(r.mate!=null){
addRead(r.mate, count, k, mask, rcomp);
}
}
//System.err.println("returning list");
cris.returnList(ln);
//System.err.println("fetching list");
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(verbose){System.err.println("Finished reading");}
cris.returnList(ln);
if(verbose){System.err.println("Returned list");}
cris.close();
if(verbose){System.err.println("Closed stream");}
if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
return count;
}
public static KCountArray2 countFastqSplit(String reads1, String reads2, int k1, int k2, int gap, int cbits, boolean rcomp, KCountArray2 count){
assert(k1+k2>=1 && k1+k2<20);
assert(gap>=0);
final int kbits1=2*k1;
final int kbits2=2*k2;
final long mask1=~((-1L)<<(kbits1));
final long mask2=~((-1L)<<(kbits2));
if(count==null){
final long cells=1L<<(kbits1+kbits2);
if(verbose){System.err.println("k1="+k1+", k2="+k2+", kbits1="+kbits1+", kbits2="+kbits2+", cells="+cells+
", mask1="+Long.toHexString(mask1)+", mask2="+Long.toHexString(mask2));}
count=new KCountArray2(cells, cbits, gap);
}
assert(count.gap==gap);
final ConcurrentReadInputStream cris;
{
FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
cris.start(); //4567
}
assert(cris!=null) : reads1;
System.err.println("Started cris");
boolean paired=cris.paired();
if(verbose){System.err.println("Paired: "+paired);}
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
if(reads!=null && !reads.isEmpty()){
Read r=reads.get(0);
assert(paired==(r.mate!=null));
}
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
//System.err.println("reads.size()="+reads.size());
for(Read r : reads){
readsProcessed++;
addReadSplit(r, count, k1, k2, mask1, mask2, gap, rcomp);
if(r.mate!=null){
addReadSplit(r.mate, count, k1, k2, mask1, mask2, gap, rcomp);
}
}
//System.err.println("returning list");
cris.returnList(ln);
//System.err.println("fetching list");
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(verbose){System.err.println("Finished reading");}
cris.returnList(ln);
if(verbose){System.err.println("Returned list");}
cris.close();
if(verbose){System.err.println("Closed stream");}
if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
return count;
}
public static void addRead(final Read r, final KCountArray2 count, final int k, final long mask, boolean rcomp){
int len=0;
long kmer=0;
byte[] bases=r.bases;
byte[] quals=r.quality;
for(int i=0; i<bases.length; i++){
byte b=bases[i];
int x=AminoAcid.baseToNumber[b];
if(x<0 || (quals!=null && quals[i]<minQuality)){
len=0;
kmer=0;
}else{
kmer=((kmer<<2)|x)&mask;
len++;
if(len>=k){
keysCounted++;
// System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
count.increment(kmer, 1);
// System.out.println(" -> "+count.read(kmer));
// System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
// array[(int)kmer]++;
// System.out.println(" -> "+array[(int)kmer]+"\n");
// assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
}
}
}
if(rcomp){
r.reverseComplement();
addRead(r, count, k, mask, false);
}
}
public static void addReadSplit(final Read r, final KCountArray2 count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
int len=0;
int shift=k2*2;
long kmer1=0;
long kmer2=0;
byte[] bases=r.bases;
byte[] quals=r.quality;
assert(kmer1>=kmer2);
// assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
int x1=AminoAcid.baseToNumber[bases[i]];
int x2=AminoAcid.baseToNumber[bases[j]];
if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
len=0;
kmer1=0;
kmer2=0;
}else{
kmer1=((kmer1<<2)|x1)&mask1;
kmer2=((kmer2<<2)|x2)&mask2;
len++;
if(len>=k1){
keysCounted++;
// System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
long key=(kmer1<<shift)|kmer2;
// System.err.println(Long.toHexString(key));
count.increment(key, 1);
// System.out.println(" -> "+count.read(kmer));
// System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
// array[(int)kmer]++;
// System.out.println(" -> "+array[(int)kmer]+"\n");
// assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
}
}
}
if(rcomp){
r.reverseComplement();
addReadSplit(r, count, k1, k2, mask1, mask2, gap, false);
}
}
public static void addReadSplit(final byte[] bases, final KCountArray2 count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
int len=0;
int shift=k2*2;
long kmer1=0;
long kmer2=0;
byte[] quals=null;
assert(kmer1>=kmer2);
// assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
int x1=AminoAcid.baseToNumber[bases[i]];
int x2=AminoAcid.baseToNumber[bases[j]];
if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
len=0;
kmer1=0;
kmer2=0;
}else{
kmer1=((kmer1<<2)|x1)&mask1;
kmer2=((kmer2<<2)|x2)&mask2;
len++;
if(len>=k1){
keysCounted++;
// System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
long key=(kmer1<<shift)|kmer2;
System.out.println(Long.toHexString(kmer1));
System.out.println(Long.toHexString(kmer2));
System.out.println(Long.toHexString(key));
count.increment(key, 1);
// System.out.println(" -> "+count.read(kmer));
// System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
// array[(int)kmer]++;
// System.out.println(" -> "+array[(int)kmer]+"\n");
// assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
}
}
}
if(rcomp){
AminoAcid.reverseComplementBasesInPlace(bases);
addReadSplit(bases, count, k1, k2, mask1, mask2, gap, false);
}
}
}
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