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looper.cpp
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looper.cpp
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/*
Looper: DNA tandem repeat identification tool
@file looper.cpp
@author Akshay Avvaru
@version 0.1 06/08/2020
*/
#include <fstream>
#include <iostream>
#include <math.h>
#include <string.h>
#include <unordered_map>
#include <vector>
#include <chrono>
#include <assert.h>
#include "utils.h"
using namespace std;
using namespace std::chrono;
// global variable
unordered_map<string, string> rClassMap;
/* Main function of LOOPER */
int main(int argc, char* argv[]) {
ios_base::sync_with_stdio(false);
string fin, fout;
uint m = 0, M = 0, cutoff = 0;
if (argc == 1) { utils::print_help(); exit (EXIT_FAILURE); }
else if (argc > 1) {
utils::parse_arguments(argc, argv, fin, fout, m, M, cutoff);
utils::length_cutoff_error(M, cutoff);
}
uint64_t gsize = 0, GC = 0;
int sequences = 0;
utils::count_seq(fin, sequences, gsize, GC); // total number of sequences
ifstream ins(fin); // input fasta file
utils::input_file_error(ins.good(), fin);
ofstream out(fout); // output file
for (int i=0; i<200; i++) { out << " "; }; out << "\n";
string line;
utils::bitSeqWindow window;
cout << endl << "Searching for tandem repeats in " << fin << endl;
cout << "Min-motif: " << m << "\t Max-motif: " << M;
cout << "\t Length-cutoff: " << cutoff << endl << endl;
uint64_t start_time = duration_cast<milliseconds>(
system_clock::now().time_since_epoch()
).count();
// integer tracking the start of the repeat
// -1 indicates no repeat is found
int start = -1;
uint atomicity; // atomicity of the repeat
uint end; // end of the repeat
uint rlen; // length of the repeat
int repeat_check; // track if the window sequence is a repeat
int numseq = 0; // current sequence number
int const BAR_WIDTH = 60; // progress of the progress bar
string motif, repeat_class, seq_name;
// NORM is require to fetch the current window sequence
uint64_t const NORM = ~(0ull) >> 2*(32-cutoff);
// non-redundant list of motifs used for checks
vector<uint> motif_checks = utils::get_motif_sizes(m, M);
const uint N = motif_checks.size();
uint64_t divisor[N]; // list of divisors
uint rem_shift[N]; // list of remainder sizes
for (int i=0; i<N; i++) {
uint d = cutoff / motif_checks[i];
uint r = cutoff % motif_checks[i];
uint64_t D = 0ull;
for (int j=0; j<d; j++) { D = D << (2*motif_checks[i]); D += 1; }
D = D << (2*r);
divisor[i] = D;
rem_shift[i] = 2*(cutoff - r);
}
while(getline(ins, line)) {
if (line[0] == '>') {
float progress = ((float) numseq) / ((float) sequences);
if (start != -1) {
end = window.count; rlen = end - start;
out << seq_name << "\t" << start << "\t" << end \
<< "\t" << repeat_class.substr(0, atomicity) << "\t" << rlen \
<< "\t" << repeat_class.substr(atomicity, 1) << "\t" \
<< rlen/atomicity << "\t" << motif << '\n';
}
seq_name = line.substr(1, line.find(' ')-1);
window.reset(); start = -1;
utils::update_progress_bar(start_time, numseq, sequences);
cout.flush();
numseq++;
}
else {
for(const auto c: line) {
switch(c) {
case 'a': case 'A': break;
case 'c': case 'C': window.seq |= 1ull; GC += 1; break;
case 'g': case 'G': window.seq |= 2ull; GC += 1; break;
case 't': case 'T': window.seq |= 3ull; break;
case 'N': case 'n':
window.seq = 0; window.cutoff = -1;
if (start != -1) {
end = window.count; rlen = end - start;
out << seq_name << "\t" << start << "\t" << end \
<< "\t" << repeat_class.substr(0, atomicity) << \
"\t" << rlen << "\t" << \
repeat_class.substr(atomicity, 1) << "\t" \
<< rlen/atomicity << "\t" << motif << '\n';
}
start = -1;
break;
default: continue;
}
window.count += 1;
window.cutoff += 1;
window.seq &= NORM;
gsize += 1;
if (window.cutoff >= cutoff) { // To be optimized
repeat_check = 0;
for (int i=0; i<N; ++i){
if ( (window.seq % divisor[i]) == ( window.seq >> rem_shift[i]) ) {
if (start == -1) {
atomicity = utils::check_atomicity(window.seq, cutoff, motif_checks[i]);
// atomicity should be greater than
// minimum motif-size
if (atomicity >= m) {
start = window.count - cutoff;
motif = utils::bit2base(window.seq, cutoff, atomicity);
if (rClassMap.find(motif) != rClassMap.end()) {
repeat_class = rClassMap[motif];
} else {
repeat_class = utils::get_repeat_class(window.seq, cutoff, atomicity, rClassMap);
}
}
}
repeat_check = 1; break;
}
}
if (repeat_check == 0 & start != -1) {
end = window.count - 1; rlen = end - start;
out << seq_name << "\t" << start << "\t" << end \
<< "\t" << repeat_class.substr(0, atomicity) << "\t" \
<< rlen << "\t" << repeat_class.substr(atomicity, 1) \
<< "\t" << rlen/atomicity << "\t" << motif << '\n';
start = -1;
}
}
window.seq <<= 2;
}
}
}
if (start != -1) {
end = window.count; rlen = end - start;
out << seq_name << "\t" << start << "\t" << end \
<< "\t" << repeat_class.substr(0, atomicity) << "\t" << rlen \
<< "\t" << repeat_class.substr(atomicity, 1) << "\t" \
<< rlen/atomicity << "\t" << motif << '\n';
}
uint64_t end_time = duration_cast<milliseconds>(
system_clock::now().time_since_epoch()
).count();
float total_time = float(end_time - start_time)/1000.0;
utils::update_progress_bar(start_time, numseq, sequences);
cout << "Total time taken: " << total_time << " seconds" << endl;
out.clear(); out.seekp(0);
out << "#FileName: " << fin << endl;
out << "#GenomeSize: " << gsize << endl;
out << "#GC%: " << (float(GC) / float(gsize))*100 << endl;
out << "#NumSeq: " << sequences;
ins.close(); out.close();
return EXIT_SUCCESS;
}