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TandemRepeatFinder.java
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TandemRepeatFinder.java
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import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Arrays;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.Map.Entry;
import java.util.HashMap;
/**
*
* @author Rajmani Arya
* Date: 8th Oct 2016
*/
public class TandemRepeatFinder {
public static int[] suffixArray(CharSequence S) {
int n = S.length();
Integer[] order = new Integer[n];
for (int i = 0; i < n; i++)
order[i] = n - 1 - i;
Arrays.sort(order, (a, b) -> Character.compare(S.charAt(a), S.charAt(b)));
int[] sa = new int[n];
int[] classes = new int[n];
for (int i = 0; i < n; i++) {
sa[i] = order[i];
classes[i] = S.charAt(i);
}
for (int len = 1; len < n; len *= 2) {
int[] c = classes.clone();
for (int i = 0; i < n; i++) {
classes[sa[i]] = i > 0 && c[sa[i - 1]] == c[sa[i]] && sa[i - 1] + len < n && c[sa[i - 1] + len / 2] == c[sa[i] + len / 2] ? classes[sa[i - 1]] : i;
}
int[] cnt = new int[n];
for (int i = 0; i < n; i++)
cnt[i] = i;
int[] s = sa.clone();
for (int i = 0; i < n; i++) {
int s1 = s[i] - len;
if (s1 >= 0)
sa[cnt[classes[s1]]++] = s1;
}
}
return sa;
}
// longest common prefixes array in O(n)
@SuppressWarnings("empty-statement")
public static int[] lcp(int[] sa, CharSequence s) {
int n = sa.length;
int[] rank = new int[n];
for (int i = 0; i < n; i++)
rank[sa[i]] = i;
int[] lcp = new int[n - 1];
for (int i = 0, h = 0; i < n; i++) {
if (rank[i] < n - 1) {
for (int j = sa[rank[i] + 1]; Math.max(i, j) + h < s.length() && s.charAt(i + h) == s.charAt(j + h); ++h);
lcp[rank[i]] = h;
if (h > 0)
--h;
}
}
return lcp;
}
public static void PrintUnitSequence(int startIndex, String dna) throws OutOfMemoryError {
int pos, len, dna_len = dna.length();
int SufArr[] = suffixArray(dna);
int LCP[] = lcp(SufArr, dna);
int K[] = new int[dna_len];
int R[] = new int[dna_len];
for (int i=1; i < dna_len; i++) {
K[i] = Math.abs(SufArr[i]-SufArr[i-1]);
R[i] = LCP[i-1]/K[i];
}
// System.out.println("Index,Period,Length,UnitLength,Unit");
for (int i=1; i < dna_len; i++) {
if (R[i] > 0) {
pos = Math.min(SufArr[i], SufArr[i-1]);
len = K[i]*(R[i]+1);
System.out.println(startIndex+pos + "," + (R[i]+1) + "," + len + "," + K[i] + ","+ dna.substring(pos, pos+K[i]));
}
}
}
public static void PrintUnit(int startIndex, String dna) throws OutOfMemoryError {
int pos, len, dna_len = dna.length();
int SufArr[] = suffixArray(dna);
int LCP[] = lcp(SufArr, dna);
int K[] = new int[dna_len];
int R[] = new int[dna_len];
for (int i=1; i < dna_len; i++) {
K[i] = Math.abs(SufArr[i]-SufArr[i-1]);
R[i] = LCP[i-1]/K[i];
}
// System.out.println("Index,Period,Length,UnitLength");
for (int i=1; i < dna_len; i++) {
if (R[i] > 0) {
pos = Math.min(SufArr[i], SufArr[i-1]);
len = K[i]*(R[i]+1);
System.out.println(startIndex+pos + "," + (R[i]+1) + "," + len + "," + K[i]);
}
}
}
public static void PrintSequence(int startIndex, String dna) throws OutOfMemoryError {
int pos, len, dna_len = dna.length();
int SufArr[] = suffixArray(dna);
int LCP[] = lcp(SufArr, dna);
int K[] = new int[dna_len];
int R[] = new int[dna_len];
for (int i=1; i < dna_len; i++) {
K[i] = Math.abs(SufArr[i]-SufArr[i-1]);
R[i] = LCP[i-1]/K[i];
}
// System.out.println("Index,Period,Length,Sequence");
for (int i=1; i < dna_len; i++) {
if (R[i] > 0) {
pos = Math.min(SufArr[i], SufArr[i-1]);
len = K[i]*(R[i]+1);
System.out.println(startIndex+pos + ","+ (R[i]+1) + "," + len + "," + dna.substring(pos, pos+len));
}
}
}
public static void PrintRange(int startIndex, String dna) throws OutOfMemoryError {
int pos, len, dna_len = dna.length();
int SufArr[] = suffixArray(dna);
int LCP[] = lcp(SufArr, dna);
int K[] = new int[dna_len];
int R[] = new int[dna_len];
for (int i=1; i < dna_len; i++) {
K[i] = Math.abs(SufArr[i]-SufArr[i-1]);
R[i] = LCP[i-1]/K[i];
}
//System.out.println("S-Index,E-Index,Period,Sequence");
for (int i=1; i < dna_len; i++) {
if (R[i] > 0 && K[i] <= 10) {
pos = Math.min(SufArr[i], SufArr[i-1]);
len = K[i]*(R[i]+1);
System.out.println(startIndex+pos+ "," +(startIndex+pos+len)+ "," + (R[i]+1) + "," +dna.substring(pos, pos+K[i]));
}
}
}
private static class WorkerThread implements Runnable {
private String dna;
private int startIndex;
public WorkerThread(int index, String dna) {
this.startIndex = index;
this.dna = dna;
}
@Override
public void run() {
PrintRange(startIndex, dna);
}
}
public static void main(String[] args) throws FileNotFoundException, IOException {
if (args.length == 0) {
System.out.println("Usage: java TandemRepeatFinder <fasta_file> [NUM_THREADS]\n\t fasta file with {A,C,G,T} only");
System.exit(1);
}
int num_threads = 8;
if (args.length == 2) {
num_threads = Integer.parseInt(args[1]);
}
File file = new File(args[0]);
ExecutorService thpool = Executors.newFixedThreadPool(8);
int size = (int)file.length();
int chunk_size = (int)Math.ceil((double)size/10000.0);
byte bytes[] = new byte[10000];
FileInputStream fis = new FileInputStream(file);
for (int i=0; i<chunk_size; i++) {
fis.read(bytes);
Runnable worker = new WorkerThread(i*10000, new String(bytes));
thpool.execute(worker);
}
thpool.shutdown();
while (!thpool.isTerminated()) {
}
}
}