extract_str_inter.cpp
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#include <fstream>
#include <iostream>
#include <regex>
#include <sys/stat.h>
#include <boost/algorithm/string.hpp>
#include "extract_user_ct.h"
#include "utils.h"
void extract_str(std::string STRfile, const std::vector < Rna >& rnaList_,
std::vector< Structure >& strs_,
const std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
const std::vector< std::tuple < uint, uint, uint > >& ctApp,
const std::vector< std::tuple < uint, uint, uint > >& ctSingle,
const std::vector < Interloop * >& ctIntLoop,
const std::vector < Hairpinloop * >& ctHairLoop,
const std::vector < Helix * >& ctHelix,
const std::vector < Multiloop * >& ctMultiLoop,
const std::vector < Pseudoknot * >& ctPseudo,
uint energyModel, uint &nbHardCT,
float lowerThresProbing, float upperThresProbing)
{
std::string name = "", structure ="", energyS ="", ctString ="", line = "";
std::vector< std::string > elements;
std::vector < Motif * > motifs;
//size_t tab, pos;
std::vector < std::pair < unsigned int, unsigned int > > listBp;
int ct = 0;
int nbCt = 0;
float IC = 0;
float energy; // ADDED
size_t j, size, k , size3;
int nLine = 0;
int i; // the RNA index
struct stat buf;
if( (stat(STRfile.c_str(), &buf) == 0))
{
nLine = 1;
std::ifstream ifs(STRfile);
while (std::getline(ifs, line))
{
if (line[0] != '\n' and line != "") // No header
{
// check the format
elements.clear();
boost::split( elements, line, boost::is_any_of(" \t"), boost::token_compress_on );
if((int(elements.size()) >= 2 and (energyModel == 1 or energyModel == 2)) or (int(elements.size()) >= 3 and energyModel == 0)) // Name \space Structure \space (CT optional) -OR- Name \space Structure \space Energy \space (CT optional)
{
energyS = "";
ctString = "";
// Recover RNA index
name = elements[0];
i = -1;
for (j = 0, size = rnaList_.size(); j != size; j++)
if (name.compare(rnaList_[j].get_name_()) == 0)
i = j;
if ( i != -1 ) { // RNA index is ok
structure = elements[1];
if(energyModel == 0) {
energyS = elements[2];
if (uint(elements.size()) >= 4) {
ctString = elements[3];
}
}
else if (uint(elements.size()) >= 3) {
ctString = elements[2];
}
// Check length structure
if(uint(structure.size()) == rnaList_[i].get_n_()) {
// Check if the structure is not empty
if(structure.compare(std::string(rnaList_[i].get_seq_().size(), '.')) != 0) {
// Check base pair A-U, G-C, G-U
try {
Structure::checkStructure(structure);
listBp.clear();
Structure::makeListBp(structure, listBp);
std::sort(listBp.begin(), listBp.end());
Structure::checkListBp(rnaList_[i].get_seq_(), listBp);
} catch (std::string e) {
throw (std::string("Secondary structure in line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n" + e));
}
if (energyModel == 0) {
try {
energy = std::stof(energyS);
}
catch (std::string e) {
throw (std::string("Energy of structure line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n"));
}
}
nbCt = 0;
ct = 0;
IC = 0;
Structure str = Structure(int(i), rnaList_[i].get_seq_(), listBp,
ct, nbCt, int(strs_.size()), energyModel, energy,
rnaList_[i].get_probingData_(), lowerThresProbing, upperThresProbing);
if((energyModel == 0 and elements.size() >= 4) or (energyModel != 0 and elements.size() >= 3)) {
try {
if (checkIC(ctString)) {
ct = std::stoi(ctString);
IC += ct;
nbCt++;
if (ct == 100)
nbHardCT++;
} else {
throw (std::string("Constraint of structure line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n"));
}
} catch (std::string e) {
throw (std::string("Constraint of structure line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n" + e));
}
}
//std::cout << "ctAppTwo"<< std::endl;
// Count the number of constraint the structure corresponds
// and count the number of hard constraint the structure doesn't correspond
bool hardCT = true;
for(j = 0, size = ctAppTwo.size(); j != size; j++) {
if(std::get<0>(ctAppTwo[j]).first == uint(i) // the structure corresponds to the ct
and std::get<1>(ctAppTwo[j]).first == uint(i)
and std::find(listBp.begin(), listBp.end(),
std::make_pair(std::get<0>(ctAppTwo[j]).second, std::get<1>(ctAppTwo[j]).second))
!= listBp.end())
{
IC += std::get<2>(ctAppTwo[j]);
nbCt++;
if (std::get<2>(ctAppTwo[j]) == 100)
ct = 100;
} else if (hardCT and std::get<2>(ctAppTwo[j]) == 100 // the structure corresponds to the ct and it's a hardCT
and (
// if same RNAs and we don't find the base pair
(std::get<0>(ctAppTwo[j]).first == uint(i)
and std::get<1>(ctAppTwo[j]).first == uint(i)
and std::find(listBp.begin(), listBp.end(),
std::make_pair(std::get<0>(ctAppTwo[j]).second, std::get<1>(ctAppTwo[j]).second))
== listBp.end())
or // if one RNA is the same and the secondary structure is in conflict with the ct
(std::get<0>(ctAppTwo[j]).first == uint(i)
and std::get<1>(ctAppTwo[j]).first != uint(i)
and !find_bp_with_i(listBp, std::get<0>(ctAppTwo[j]).second).empty())
or // same but other rna
(std::get<0>(ctAppTwo[j]).first != uint(i)
and std::get<1>(ctAppTwo[j]).first == uint(i)
and !find_bp_with_i(listBp, std::get<1>(ctAppTwo[j]).second).empty())
)){
hardCT = false;
}
}
//std::cout << "ctAppS"<< std::endl;
for(j = 0, size = ctApp.size(); j != size; j++) {
if(std::get<0>(ctApp[j]) == uint(i)
and !find_bp_with_i(listBp, std::get<1>(ctApp[j])).empty())
{
IC += std::get<2>(ctApp[j]);
nbCt++;
if (std::get<2>(ctApp[j]) == 100)
ct = 100;
} else if(hardCT and std::get<2>(ctApp[j]) == 100
// same RNA but the base is single
and (std::get<0>(ctApp[j]) == uint(i)
and find_bp_with_i(listBp, std::get<1>(ctApp[j])).empty())
){
hardCT = false;
}
}
//std::cout << "ctSingleS"<< std::endl;
for(j = 0, size = ctSingle.size(); j != size; j++){
if((std::get<0>(ctSingle[j]) == uint(i) and !find_i_at_first(listBp, std::get<1>(ctSingle[j])))
or (std::get<0>(ctSingle[j]) == uint(i) and !find_i_at_second(listBp, std::get<1>(ctSingle[j]))))
{
IC += std::get<2>(ctSingle[j]);
nbCt++;
if (std::get<2>(ctSingle[j]) == 100)
ct = 100;
} else if (hardCT and std::get<2>(ctSingle[j]) == 100
// same RNA and the base isn't single
and (std::get<0>(ctSingle[j]) == uint(i)
and !find_bp_with_i(listBp, std::get<1>(ctSingle[j])).empty())) {
hardCT = false;
}
}
// Determine motifs
//std::cout << "Motif"<< std::endl;
motifs = str.get_motifs_();
for(k = 0, size3 = motifs.size(); k != size3; k++) {
if (Helix * S = dynamic_cast < Helix * > (motifs[k])) {
//std::cout << "Helix"<< std::endl;
for(j = 0, size = ctHelix.size(); j != size; j++) {
if (S->compCt(ctHelix[j])) {
IC += ctHelix[j]->getIc_();
nbCt++;
if (ctHelix[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctHelix[j]->getIc_() == 100) {
hardCT = false;
}
}
}
else if (Interloop * I = dynamic_cast < Interloop * > (motifs[k])) {
//std::cout << "Interloop"<< std::endl;
for(j = 0, size = ctIntLoop.size(); j != size; j++) {
if (I->compCt(ctIntLoop[j])) {
IC += ctIntLoop[j]->getIc_();
nbCt++;
if (ctIntLoop[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctIntLoop[j]->getIc_() == 100) {
hardCT = false;
}
}
}
else if (Hairpinloop * H = dynamic_cast < Hairpinloop * > (motifs[k])) {
//std::cout << "Hairpin"<< std::endl;
for(j = 0, size = ctHairLoop.size(); j != size; j++) {
if (H->compCt(ctHairLoop[j])) {
IC += ctHairLoop[j]->getIc_();
nbCt++;
if (ctHairLoop[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctHairLoop[j]->getIc_() == 100) {
hardCT = false;
}
}
}
else if (Pseudoknot * P = dynamic_cast < Pseudoknot * > (motifs[k])) {
//std::cout << "Pseudonoeud"<< std::endl;
for(j = 0, size = ctPseudo.size(); j != size; j++) {
if (P->compCt(ctPseudo[j])) {
IC += ctPseudo[j]->getIc_();
nbCt++;
if (ctPseudo[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctPseudo[j]->getIc_() == 100) {
hardCT = false;
}
}
}
else if (Multiloop * M = dynamic_cast < Multiloop * > (motifs[k])) {
//std::cout << "Multiloop"<< std::endl;
for(j = 0, size = ctMultiLoop.size(); j != size; j++) {
if (M->compCt(ctMultiLoop[j])) {
IC += ctMultiLoop[j]->getIc_();
nbCt++;
if (ctMultiLoop[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctMultiLoop[j]->getIc_() == 100) {
hardCT = false;
}
}
}
}
// Compute IC
/*#ifdef _DEBUG
std::cout << "IC " << IC << " nbCt " << nbCt << std::endl;
#endif*/
if (nbCt != 0)
IC = IC; // / float(nbCt);
else
IC = 0; // Default confidence index is equal to 0
/*#ifdef _DEBUG
std::cout << "STR " << nLine << " " << IC << " " << str.get_probing_() << " " << str.get_obj1_() << std::endl;
#endif*/
hardCT = true; // TO IGNORE THE HARD CONSTRAINTS ASPECT, REMOVE TO GO BACK TO ORIGINAL
if (hardCT) {
str.set_ct_(ct);
str.set_nbCt_(nbCt);
str.set_ic_(IC);
strs_.push_back(str);
}
}
}
else
{
throw (std::string("The length of RNA " + std::to_string(i) + " is not the same of the secondary structures in line " +
std::to_string(nLine) + "."));
}
} else {
throw (std::string("The RNA " + name + " does not exist in the fasta file. Found in structure file line " +
std::to_string(nLine) + "."));
}
}
else
{
throw (std::string("The format of the secondary structure line " + std::to_string(nLine) +
" is not correct. Please look at the example inputs."));
}
}
nLine++;
}
}
else
{
throw(std::string("The file " + STRfile + " doesn't exist."));
}
}
bool sortHelix (Helix i, Helix j) {
return i.getI1_() < j.getI1_();
}
void extract_inter(const std::string INTfile, const std::vector < Rna >& rnaList_,
std::vector< SolInteraction >& inters_,
std::vector< std::vector < Helix > >& helices_,
const std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
const std::vector < Helix * >& ctHelix,
const std::vector < Pseudoknot * >& ctPseudo,
unsigned int energyModel, uint &nbHardCT,
float lowerThresProbing, float upperThresProbing)
{
std::string seq = "", name1 = "", name2 = "", line = "", structure = "", energyS = "", ctString = "";
std::vector < std::string > elements;
std::vector < Motif * > motifs;
unsigned int nbCt = 0;
int rna1 = -1, rna2 = -1;
int ct = 0;
float IC = 0;
float energy;
size_t j, size, k, size2;
std::vector< std::vector < Helix > > helicesBis;
// Initialize helices_ vector for G2 graph
std::vector < std::vector < uint > > combis;
uint counter = 0;
for(size_t rna1 = 0, size = rnaList_.size(); rna1 != size; rna1++)
for (size_t rna2 = 0, size2 = rnaList_.size(); rna2 != size2; rna2++) {
combis.push_back(std::vector < uint > (rnaList_.size()));
if (rna1 < rna2) {
helices_.push_back(std::vector < Helix > ());
helicesBis.push_back(std::vector < Helix > ());
combis[rna1][rna2] = counter;
counter++;
}
}
// Extract data
struct stat buf;
if( (stat(INTfile.c_str(), &buf) == 0))
{
int nLine = 1;
std::ifstream ifs(INTfile);
while (std::getline(ifs, line))
{
if (line[0] != '\n' and line != "") // No header
{
// Check the format
elements = std::vector < std::string > ();
boost::split(elements, line, boost::is_any_of(" \t"), boost::token_compress_on );
if((energyModel == 0 and int(elements.size()) >= 4) or (energyModel != 0 and int(elements.size()) >= 3)) // Name1 \space Name2 \space Structure \space Energy \space (CT optional) -OR- Name1 \space Name2 \space Structure \space (CT optional)
{
// Check RNA indexes
name1 = "";
name2 = "";
name1 = elements[0];
name2 = elements[1];
rna1 = -1;
rna2 = -1;
for (j = 0, size = rnaList_.size(); j != size; j++)
if (name1.compare(rnaList_[j].get_name_()) == 0)
rna1 = j;
for (j = 0, size = rnaList_.size(); j != size; j++)
if (name2.compare(rnaList_[j].get_name_()) == 0)
rna2 = j;
if ( rna1 != -1 and rna2 != -1 ) { // RNA indexes are ok
structure = "";
energyS = "";
ctString = "";
structure = elements[2];
if(energyModel == 0) {
energyS = elements[3];
if (elements.size() >= 5) {
ctString = elements[5];
}
}
else if (elements.size() >= 4) {
ctString = elements[3];
}
seq = rnaList_[rna1].get_seq_() + "&" + rnaList_[rna2].get_seq_();
if(int(structure.size()) == int(seq.size())) {
if(ctString.compare("U") != 0 and
structure.compare(
std::string(rnaList_[rna1].get_seq_().size(), '.') + "&" +
std::string(rnaList_[rna2].get_seq_().size(), '.')) != 0) {
std::vector < std::pair < unsigned int, unsigned int > > listBp;
try {
SolInteraction::checkStructure(structure);
listBp = SolInteraction::convToBP(std::string(structure));
SolInteraction::checkListBp(rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_(), listBp);
} catch (std::string e) {
throw (std::string("Interaction in line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n" + e));
}
if (energyModel == 0) {
try {
energy = std::stof(energyS);
}
catch (std::string e) {
throw (std::string("Energy of interaction line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n"));
}
}
if( int(listBp.size()) > 0 ) {
nbCt = 0; //nb de contrainte
ct = 0; // indice de confiance de l'interaction seule
IC = 0; // indice de confiance de l'interaction seule + ct du fichier utilisateur
//std::cout << "Création SolInteraction" << std::endl;
SolInteraction sol = SolInteraction(rna1, rna2, rnaList_[rna1].get_seq_(),
rnaList_[rna2].get_seq_(), listBp,
ct, nbCt, uint(inters_.size()),
energyModel, energy,
rnaList_[rna1].get_probingData_(),
rnaList_[rna2].get_probingData_(),
lowerThresProbing, upperThresProbing);
//std::cout << "Fin création SolInteraction" << std::endl;
// If constraint
if((energyModel == 0 and elements.size() >= 5) or (energyModel != 0 and elements.size() >= 4)) {
try {
if (checkIC(ctString)) {
ct = std::stoi(ctString);
IC += ct;
nbCt++;
if (ct == 100)
nbHardCT++;
} else {
throw (std::string("Constraint of interaction line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n"));
}
} catch (std::string e) {
throw (std::string("Constraint of interaction line " + std::to_string(nLine) +
" is not valid. Please correct this input.\n" + e));
}
}
//std::cout << "Apres If constraint" << std::endl;
// Count the number of constraint the solInteraction corresponds
// and count the number of hard constraint the structure doesn't correspond
bool hardCT = true;
for(j = 0, size = ctAppTwo.size(); j != size; j++) {
if(std::get<0>(ctAppTwo[j]).first == rna1
and std::get<1>(ctAppTwo[j]).first == rna2
and std::find(listBp.begin(), listBp.end(),
std::make_pair(std::get<0>(ctAppTwo[j]).second,
std::get<1>(ctAppTwo[j]).second)) != listBp.end())
{
//std::cout << "ctAppTwo add dans inter" << std::endl;
IC += std::get<2>(ctAppTwo[j]);
nbCt++;
if (std::get<2>(ctAppTwo[j]) == 100)
ct = 100;
} else if (hardCT and std::get<2>(ctAppTwo[j]) == 100
and (
// if same RNAs and we don't find the base pair
(std::get<0>(ctAppTwo[j]).first == rna1
and std::get<1>(ctAppTwo[j]).first == rna2
and std::find(listBp.begin(), listBp.end(),
std::make_pair(std::get<0>(ctAppTwo[j]).second, std::get<1>(ctAppTwo[j]).second))
== listBp.end())
or // if one RNA is the same and the secondary structure is in conflict with the ct
(std::get<0>(ctAppTwo[j]).first == rna1
and std::get<1>(ctAppTwo[j]).first != rna2
and find_i_at_first(listBp, std::get<0>(ctAppTwo[j]).second))
or // same but other rna
(std::get<0>(ctAppTwo[j]).first != rna1
and std::get<1>(ctAppTwo[j]).first == rna2
and find_i_at_second(listBp, std::get<1>(ctAppTwo[j]).second))
)){
hardCT = false;
}
}
//std::cout << "Determine the number of motifs" << std::endl;
// Determine the number of motifs
motifs = sol.get_motifs_();
int nbHelices = 0;
for(k = 0, size = motifs.size(); k != size; k++)
{
if (Helix * S = dynamic_cast < Helix * > (motifs[k]))
{
Helix s = (*S);
// Recover the helices for graph G2
s.setIdSolInter_(inters_.size());
s.setId_(helicesBis[combis[rna1][rna2]].size());
helicesBis[combis[rna1][rna2]].push_back(s);
nbHelices++;
//std::cout << "Inter line " << nLine << " rna1 " << rna1 << " rna2 " << rna2 << " combi "
// << combis[rna1][rna2] << " " << s.convToDP() << std::endl;
// constraints
for(j = 0, size2 = ctHelix.size(); j != size2; j++) {
if (S->compCt(ctHelix[j])) {
IC += ctHelix[j]->getIc_();
nbCt++;
if (ctHelix[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctHelix[j]->getIc_() == 100) {
hardCT = false;
}
}
}
else if (Pseudoknot * P = dynamic_cast < Pseudoknot * > (motifs[k]))
{
for(j = 0, size2 = ctPseudo.size(); j != size2; j++) {
if (P->compCt(ctPseudo[j]))
{
IC += ctPseudo[j]->getIc_();
nbCt++;
if (ctPseudo[j]->getIc_() == 100)
ct = 100;
} else if(hardCT and ctPseudo[j]->getIc_() == 100) {
hardCT = false;
}
}
}
}
// Compute IC
if (nbCt != 0)
IC = IC;// / float(nbCt);
else
IC = 0; // Default confidence index is equal to 0
//std::cout << "apres determine motifs" << std::endl;
#ifdef _DEBUG
std::cout << "INTER " << nLine << " " << IC << " " << sol.get_probing_() << " " << sol.get_score_() << " " << sol.get_ct_() << std::endl;
std::cout << sol.to_string() << std::endl;
#endif
hardCT = true; // TO IGNORE THE HARD CONSTRAINTS ASPECT, REMOVE TO GO BACK TO ORIGINAL
if (hardCT) { // s'il y a des hardCT et que la structure/inter ne correspond à aucune alors elle est pas dans le graphe
helices_[combis[rna1][rna2]] = helicesBis[combis[rna1][rna2]];
sol.set_ct_(ct);
sol.set_nbCt_(nbCt);
sol.set_ic_(IC);
inters_.push_back(sol);
} else {
for(j = 0; j != nbHelices; j++)
helicesBis[combis[rna1][rna2]].pop_back();
}
//std::cout << "Num vertex " << inters_.size() << std::endl;
}
}
}
else
{
throw (std::string("The length of the interaction of RNA " + name1 +
" and RNA " + name2 + " does not correspond with the fasta file. Found line "
+ std::to_string(nLine) + "."));
}
} else if (rna1 == -1 and rna2 == -1) {
throw (std::string("The RNAs " + name1 + " and " + name2 + " do not exist in the fasta file. Found in interaction file line " +
std::to_string(nLine) + "."));
} else if (rna1 == -1) {
throw (std::string("The RNA " + name1 + " does not exist in the fasta file. Found in interaction file line " +
std::to_string(nLine) + "."));
} else {
throw (std::string("The RNA " + name2 + " does not exist in the fasta file. Found in interaction file line " +
std::to_string(nLine) + "."));
}
}
else
{
throw (std::string("The format of the interaction file " + INTfile + " is not correct. Please look at the example inputs."));
}
}
nLine++;
}
#ifdef _DEBUG
std::cout << "avant sort helices" << std::endl;
#endif
// Sort Helices_ for G2 graph
for(uint i = 0, size = helices_.size(); i != size; i++) {
#ifdef _DEBUG
std::cout << "combi " << i << " : ";
#endif
std::sort(helices_[i].begin(), helices_[i].end(), sortHelix);
#ifdef _DEBUG
for (uint j = 0, size2 = helices_[i].size(); j != size2; j++)
std::cout << helices_[i][j].getId_() << " ";
std::cout << std::endl;
#endif
}
}
else
{
throw (std::string("The file " + INTfile + " doesn't exist."));
}
}