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vari_rest_kmers.cpp
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vari_rest_kmers.cpp
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#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <libgen.h> // basename
#include "tclap/CmdLine.h"
#include <sdsl/bit_vectors.hpp>
#include <sdsl/wavelet_trees.hpp>
#include "io.hpp"
#include "debruijn_graph_shifted.hpp"
#include "algorithm.hpp"
#include "cosmo-color.hpp"
using namespace std;
using namespace sdsl;
#include <sys/timeb.h>
int getMilliCount(){
timeb tb;
ftime(&tb);
int nCount = tb.millitm + (tb.time & 0xfffff) * 1000;
return nCount;
}
int getMilliSpan(int nTimeStart){
int nSpan = getMilliCount() - nTimeStart;
if(nSpan < 0)
nSpan += 0x100000 * 1000;
return nSpan;
}
//void parse_arguments(int argc, char **argv, parameters_t & params)
//{
// TCLAP::CmdLine cmd(BANNER, ' ', VERSION);
// TCLAP::UnlabeledValueArg<std::string> input_filename_arg("input", ".dbg file.", true, "", "graph_file", cmd);
// TCLAP::UnlabeledValueArg<std::string> color_filename_arg("color", ".rrr file.", true, "", "color_file", cmd);
// string color_mask1 = "color_mask1";
// TCLAP::ValueArg<std::string> color_mask1_arg("a", "color_mask1",
// "Color mask 1, color1 [" + color_mask1 + "]", false, "", color_mask1, cmd);
// string color_mask2 = "color_mask2";
// TCLAP::ValueArg<std::string> color_mask2_arg("b", "color_mask2",
// "Color mask 2, color2 [" + color_mask2 + "]", false, "", color_mask2, cmd);
// cmd.parse( argc, argv );
//
// params.input_filename = input_filename_arg.getValue();
// params.color_filename = color_filename_arg.getValue();
// params.color_mask1 = color_mask1_arg.getValue();
// params.color_mask2 = color_mask2_arg.getValue();
//}
void parse_arguments(int argc, char **argv, parameters_t & params)
{
TCLAP::CmdLine cmd("Opgraph Copyright (c) Kingshuk Mukherjee 2017", ' ', VERSION);
TCLAP::UnlabeledValueArg<std::string> input_filename_arg("input",
".packed edge file (output from pack-edges).", true, "", "input_file", cmd);
TCLAP::ValueArg<std::string> restriction_enzyme_arg("o", "restriction_enzyme",
"restriction_enzyme", true, "", "restriction_enzyme", cmd);
cmd.parse( argc, argv );
params.input_filename = input_filename_arg.getValue();
params.restriction_seq = restriction_enzyme_arg.getValue();
}
static char base[] = {'?','A','C','G','T'};
void test_symmetry(debruijn_graph_shifted<> dbg) {
for (unsigned long x = 0; x<dbg.sigma+1;x++) {
ssize_t in = dbg.incoming(43, x);
if (in == -1)
continue;
for (unsigned long y = 0; y<dbg.sigma+1;y++) {
ssize_t out = dbg.outgoing(in, y);
if (out == -1)
continue;
cout << "Incoming " << in << ":" << out <<"\n";
}
}
}
void dump_nodes(debruijn_graph_shifted<> dbg, uint64_t * colors) {
for (size_t i = 0; i < dbg.num_nodes(); i++) {
cout << i << ":" << dbg.node_label(i) << colors[dbg._node_to_edge(i)] << "\n";
}
}
void dump_edges(debruijn_graph_shifted<> dbg, uint64_t * colors) {
for (size_t i = 0; i < dbg.size(); i++) {
cout << i << "e:" << dbg.edge_label(i) << colors[i] << "\n";
}
}
const char *const starts[] = {"GCCATACTGCGTCATGTCGCCCTGACGCGC","GCAGGTTCGAATCCTGCACGACCCACCAAT","GCTTAACCTCACAACCCGAAGATGTTTCTT","AAAACCCGCCGAAGCGGGTTTTTACGTAAA","AATCCTGCACGACCCACCAGTTTTAACATC","AGAGTTCCCCGCGCCAGCGGGGATAAACCG","GAATACGTGCGCAACAACCGTCTTCCGGAG"};
void print_color(color_bv& color)
{
std::string colstr = color.to_string();
for (unsigned int first1 = 0; first1 < colstr.size() ; first1++) {
if (colstr[first1] == '1') {
std::string outstring = colstr.substr(first1, colstr.size());
cout << outstring;
return;
}
}
cout << "0";
}
void find_bubbles(const debruijn_graph_shifted<> &dbg, sd_vector<> &colors, color_bv color_mask1, color_bv color_mask2)
{
int t = getMilliCount();
int num_colors = colors.size() / dbg.size();
sdsl::bit_vector visited = sdsl::bit_vector(dbg.num_nodes(), 0);
cout << "Starting to look for bubbles\n";
std::vector<std::string> branch_labels(2);
// for each candidate start nodein the graph
for (size_t start_node = 0; start_node < dbg.num_nodes(); start_node++) {
// if its out degree is two and we haven't encountered it already, start processing it like it's the start of a bubble
if (!visited[start_node] && dbg.outdegree(start_node) == 2) { //FIXME: why do we only care about outdegree == 2?
// initialize bubble tracking variables
color_bv branch_color[2];
size_t end_nodes[2]; // AKA right flank start. place to store end of branch node
// start of a bubble handling
int branch_num = -1;
for (unsigned long x = 1; x < dbg.sigma + 1; x++) { // iterate through the DNA alphabet looking for *the* two outgoing edges from node i
// follow each strand or supernode
ssize_t edge = dbg.outgoing_edge(start_node, x);
if (edge == -1)
continue;
branch_num++;
branch_labels[branch_num].clear();
branch_labels[branch_num] += base[x];
// build color mask
color_bv color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[edge * num_colors + c] << c;
branch_color[branch_num] = color_mask;
// walk along edges until we encounter
ssize_t pos = dbg._edge_to_node(edge);
while (dbg.indegree(pos) == 1 && dbg.outdegree(pos) == 1) {
visited[pos] = 1;
ssize_t next_edge = 0;
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) { // iterate through the alphabet
next_edge = dbg.outgoing_edge(pos, x2);
if (next_edge != -1) {
branch_labels[branch_num] += base[x2];
break;
}
}
pos = dbg._edge_to_node(next_edge);
}
// if we stopped walking along the bubble on a node where indegree > 1, then record this new node
end_nodes[branch_num] = (dbg.indegree(pos) > 1) ? pos : 0;
}
// check same end node
if ((end_nodes[0] && end_nodes[0] == end_nodes[1]) ) {
// check color:
if (((color_mask1 & branch_color[0]).any() && (~color_mask1 & branch_color[0]).none() &&
(color_mask2 & branch_color[1]).any() && (~color_mask2 & branch_color[1]).none()) ||
((color_mask1 & branch_color[1]).any() && (~color_mask1 & branch_color[1]).none() &&
(color_mask2 & branch_color[0]).any() && (~color_mask2 & branch_color[0]).none())) {
cout << "\nStart flank: " << dbg.node_label(start_node) << " c: ";
print_color ( branch_color[0]);
cout << ":";
print_color( branch_color[1]);
cout << "\n";
cout << "Branch: " << branch_labels[0] << "\n";
cout << "Branch: " << branch_labels[1] << "\n";
cout << "End flank: " << dbg.node_label(end_nodes[0]) << "\n";
}
}
}
}
cerr << "Find bubbles time: " << getMilliSpan(t) << std::endl;
}
void find_restriction_kmers(debruijn_graph_shifted<> dbg, string restriction_enzyme)
{
ofstream ofile;
ofile.open("restriction_nodes2");
int cnt=0;
for (size_t i = 0; i < dbg.num_nodes(); i++) {
if(i%100000==0)
cout<<i<<" "<<cnt<<endl;
ssize_t start = i; // place to store start of branch kmer
std::string start_label(dbg.node_label(start));
if(start_label.compare(0,restriction_enzyme.length(),restriction_enzyme)==0){
ofile<<i<<" "<<start_label<<endl;
cnt++;
}
}
}
int main(int argc, char* argv[]) {
parameters_t p;
parse_arguments(argc, argv, p);
cerr << "loading dbg" << std::endl;
debruijn_graph_shifted<> dbg;
load_from_file(dbg, p.input_filename);
cout<<"Number of nodes:"<<dbg.num_nodes()<<endl;
cout<<"Number of edges:"<<dbg.num_edges()<<endl;
string restriction_enzyme = p.restriction_seq;
find_restriction_kmers(dbg, restriction_enzyme);
return 1;
//input.close();
// cerr << "loading colors" << std::endl;
// sd_vector<> colors;
// load_from_file(colors, p.color_filename);
//
// cerr << "k : " << dbg.k << endl;
// cerr << "num_nodes() : " << dbg.num_nodes() << endl;
// cerr << "num_edges() : " << dbg.num_edges() << endl;
// cerr << "colors : " << colors.size() / dbg.size() << endl;
// cerr << "Total size : " << size_in_mega_bytes(dbg) << " MB" << endl;
// cerr << "Bits per edge : " << bits_per_element(dbg) << " Bits" << endl;
// cerr << "Color size : " << size_in_mega_bytes(colors) << " MB" << endl;
//
// //dump_nodes(dbg, colors);
// //dump_edges(dbg, colors);
// color_bv mask1 = (p.color_mask1.length() > 0) ? atoi(p.color_mask1.c_str()) : -1;
// color_bv mask2 = (p.color_mask2.length() > 0) ? atoi(p.color_mask2.c_str()) : -1;
// find_bubbles(dbg, colors, mask1, mask2);
}