selecting_id.cpp
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#include <iostream>
#include <sstream>
#include <fstream>
#include "/mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/cppsrc/json.hpp"
#include <typeinfo>
#include <set>
#include <algorithm>
#include <cstdio>
#include <vector>
using namespace std;
using json = nlohmann::json;
/*
That script will remove from the library all the pattern that match ONLY with the sequence from which it comes from (with the same pdb).
*/
//To store the pdb and the sequence in the benchmark file. Also stor the corresponding motif id and components based on this sequence.
struct data {
//the pdb code (in the name of the sequence)
string pdb;
//the complete sequence with this pdb code
string seq_pdb;
//the id of the motif corresponding to this pdb in the library
string id;
//the module sequence with the components of this motif with the above id
string cmp;
};
typedef struct data data;
//returns the list of pdb codes and the corresponding information from the benchmark file.
vector<data> get_list_pdb_benchmark(const string& benchmark) {
fstream bm(benchmark);
vector<data> list_pdb_seq;
if (bm.is_open()) {
string name;
string sequence;
string structure;
string contacts;
while (getline(bm, name)) {
data d;
int size = name.size();
name = name.substr(5,size-6);
getline(bm, sequence);
d.pdb = name;
d.seq_pdb = sequence;
list_pdb_seq.push_back(d);
getline(bm, structure);
getline(bm, contacts);
}
bm.close();
}
return list_pdb_seq;
}
string trim(string str) {
int size = str.size();
str = str.substr(1, size-2);
return str;
}
//store the corresponding id and motif to the sequence from the benchmark file
data find_id_pattern(string& pdb_pattern, const string& benchmark) {
vector<data> l = get_list_pdb_benchmark(benchmark);
int size = l.size();
for (data d : l) {
string cmp = d.pdb;
cmp = cmp.substr(0, d.pdb.size()-2);
if (!cmp.compare(pdb_pattern)) {
return d;
}
}
return data();
}
//Create an array of data ('association'), which consists of each pdb of the benchmark file
// with the associated pattern from this sequence.
vector<data> find_id(const string& bibli, const string& benchmark) {
ifstream lib(bibli);
json js = json::parse(lib);
//nam seq_bm et id seq_id
vector<data> association;
for (auto it = js.begin(); it != js.end(); ++it) {
string id = it.key();
data d;
for (auto it2 = js[id].begin(); it2 != js[id].end(); ++it2) {
string field = it2.key();
string seq;
if (!field.compare("pdb")) {
int n = js[id][field].size();
for (int i = 0; i < n ; i++) {
ostringstream stream;
stream << js[id][field][i];
string pdb = trim(stream.str());
d = find_id_pattern(pdb, benchmark);
}
}
if (!field.compare("sequence")) {
seq = it2.value();
if (!(d.pdb.empty())) {
d.id = id;
d.cmp = seq;
association.push_back(d);
}
}
}
}
lib.close();
cout << association.size() << endl;
return association;
}
//check if the motif is found matching with a complete sequence from a benchmark file.
bool does_it_match(const string& seq, const string& seq_motif) {
size_t found = seq_motif.find("&");
size_t size = seq_motif.size();
vector<string> list_cmp;
if (found != std::string::npos) {
int count = 1;
string cmp = seq_motif.substr(0, found);
list_cmp.push_back(cmp);
while(found != std::string::npos) {
size_t begin = found;
found = seq_motif.find("&", found + 1);
cmp = seq_motif.substr(begin+1, found-begin-1);
list_cmp.push_back(cmp);
count++;
}
found = seq.find(list_cmp[0]);
int count2 = 1;
while((found != std::string::npos) && (count2 < count)) {
size_t begin = found;
found = seq.find(list_cmp[count2], found + 1);
count2++;
}
if(count == count2) {
return true;
}
} else {
found = seq.find(seq_motif);
if (found != std::string::npos) {
return true;
}
}
return false;
}
//return the list of motif id that didn't match with any other complete sequence than the one which it came from.
vector<string> select_not_motif(const string& bibli, const string& benchmark) {
vector<string> selection;
vector<data> association = find_id(bibli, benchmark);
for (data d : association) {
selection.push_back(d.id);
}
for (data d : association) {
for (data d2 : association) {
string seq = d.seq_pdb;
string seq2 = d2.cmp;
bool test = false;
if(d.pdb.substr(0, d.pdb.size()-2) != d2.pdb.substr(0, d2.pdb.size()-2)) {
test = does_it_match(seq, seq2);
if (test) {
cout << "pdb: " << d.pdb << " vs " << d2.pdb << " " << d2.cmp << " " << d2.id << endl;
auto position = find(selection.begin(), selection.end(), d.id);
if (position != selection.end()) {
int index = position - selection.begin();
selection.erase(selection.begin() + index);
}
}
}
}
}
sort(selection.begin(), selection.end() );
selection.erase(unique(selection.begin(), selection.end() ), selection.end() );
cout << "size: " << selection.size() << endl;
return selection;
}
int main()
{
string bibli = "/mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/ISAURE/motifs_final.json";
string benchmark = "/mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/benchmark.dbn";
/*vector<data> v = get_list_pdb_benchmark(benchmark);
for (data d : v) {
cout << d.pdb << ", " << d.seq_pdb << endl;
}*/
/*string name = "1U6P_B";
data d = find_id_pattern(name, benchmark);
cout << "name: " << d.pdb << ", seq: " << d.seq_pdb << endl;*/
/*vector<data> association = find_id(bibli, benchmark);
for (data d : association) {
cout << "<" << d.pdb << ", " << d.seq_pdb << ">, " << "<" << d.id << ", " << d.cmp << ">" << endl;
}*/
/*string seq = "UGCGCUUGGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU";
string seq_motif = "UGCGCUUGGCGUUUUAGAGC&GCAAGUUAAAAUAAGGCUAGUCCGUUAUCAA&UGGCACCGAGUCG&U";
bool test = does_it_match(seq, seq_motif);
cout << test << endl;*/
vector<string> selection = select_not_motif(bibli, benchmark);
for (string str : selection) {
cout << str << ", ";
}
cout << endl;
return 0;
}