biominserter.cpp
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/***
Biominserter, Louis Becquey, nov 2018
***/
#include <algorithm>
#include <boost/program_options.hpp>
#include <cstdlib>
#include <iostream>
#include <iterator>
#include <string>
#include <vector>
#include "MOIP.h"
#include "Motif.h"
#include "fa.h"
using namespace std;
namespace po = boost::program_options;
string remove_ext(const char* mystr, char dot, char sep)
{
// COPYPASTA from stackoverflow
char *retstr, *lastdot, *lastsep;
// Error checks and allocate string.
if (mystr == nullptr) return nullptr;
if ((retstr = static_cast<char*>(malloc(strlen(mystr) + 1))) == nullptr) return nullptr;
// Make a copy and find the relevant characters.
strcpy(retstr, mystr);
lastdot = strrchr(retstr, dot);
lastsep = (sep == 0) ? nullptr : strrchr(retstr, sep);
// If it has an extension separator.
if (lastdot != nullptr) {
// and it's before the extenstion separator.
if (lastsep != nullptr) {
if (lastsep < lastdot) {
// then remove it.
*lastdot = '\0';
}
} else {
// Has extension separator with no path separator.
*lastdot = '\0';
}
}
// Return the modified string.
return string(retstr);
}
int main(int argc, char* argv[])
{
/* VARIABLE DECLARATIONS */
string inputName, outputName, motifs_path_name, basename;
bool verbose = false;
float theta_p_threshold;
int obj_function_nbr = 3;
list<Fasta> f;
vector<Motif> posInsertionSites;
ofstream outfile;
SecondaryStructure bestSSO1, bestSSO2;
RNA myRNA;
/* ARGUMENT CHECKING */
po::options_description desc("Options");
desc.add_options()("help,h", "Print the help message")("version", "Print the program version")(
"seq,s", po::value<string>(&inputName)->required(), "Fasta file containing the RNA sequence")(
"descfolder,d",
po::value<string>(&motifs_path_name),
"A folder containing modules in .desc format, as produced by Djelloul & Denise's catalog program")(
"jar3dcsv",
po::value<string>(&motifs_path_name),
"A file containing the output of JAR3D's search for motifs in the sequence, as produced by test_on_RNAstrand.py")(
"bayespaircsv",
po::value<string>(&motifs_path_name),
"A file containing the output of BayesPairing's search for motifs in the sequence, as produced by "
"test_on_RNAstrand.py")("first-objective,c", po::value<unsigned int>(&MOIP::obj_to_solve_)->default_value(1), "Objective to solve in the mono-objective portions of the algorithm")(
"output,o", po::value<string>(&outputName), "A file to summarize the computation results")(
"theta,t",
po::value<float>(&theta_p_threshold)->default_value(0.001),
"Pairing probability threshold to consider or not the possibility of pairing")(
"type",
po::value<int>(&obj_function_nbr),
"If -f is provided, what objective function to use to include motifs: square of motif size in nucleotides like "
"RNA-MoIP (1), jar3d score (2), motif size + jar3d score + number of components (3), motif size + number of "
"components (4)")("verbose,v", "Print what is happening to stdout");
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
basename = remove_ext(inputName.c_str(), '.', '/');
try {
po::store(po::parse_command_line(argc, argv, desc), vm); // can throw
if (vm.count("help") or vm.count("-h")) {
cout << "Biominserter, bio-objective integer linear programming framework to predict RNA secondary "
"structures with included known RNA modules."
<< endl
<< "developped by Louis Becquey (louis.becquey@univ-evry.fr), 2019" << endl
<< "NOTE THIS VERSION IS SUPPOSED TO MIMIC RNA MoIP (input data, objective functions, constraints)" << endl
<< endl
<< desc << endl;
return EXIT_SUCCESS;
}
if (vm.count("version")) {
cout << "Biominserter RNA-MoIP special edition, 2019" << endl;
return EXIT_SUCCESS;
}
if (vm.count("verbose")) verbose = true;
if (!vm.count("jar3dcsv") and !vm.count("bayespaircsv") and !vm.count("descfolder")) {
cerr << "\033[31mYou must provide at least --jar3dcsv, --bayespaircsv or --descfolder.\033[0m See --help "
"for more "
"information."
<< endl;
return EXIT_FAILURE;
}
if (vm.count("-d") and (obj_function_nbr == 2 or obj_function_nbr == 3)) {
cerr << "\033[31mYou must provide --jar3dcsv or --bayespaircsv to use --type 2 or --type 3.\033[0m See "
"--help for more "
"information."
<< endl;
return EXIT_FAILURE;
}
po::notify(vm); // throws on error, so do after help in case there are any problems
} catch (po::error& e) {
cerr << "ERROR: \033[31m" << e.what() << "\033[0m" << endl;
cerr << desc << endl;
return EXIT_FAILURE;
}
MOIP::obj_function_nbr_ = obj_function_nbr;
/* FILE PARSING */
// load fasta file
if (verbose) cout << "Reading input files..." << endl;
if (access(inputName.c_str(), F_OK) == -1) {
cerr << "\033[31m" << inputName << " not found\033[0m" << endl;
return EXIT_FAILURE;
}
Fasta::load(f, inputName.c_str());
list<Fasta>::iterator fa = f.begin();
if (verbose) cout << "loading " << fa->name() << "..." << endl;
myRNA = RNA(fa->name(), fa->seq(), verbose);
if (verbose) cout << "\t>" << inputName << " successfuly loaded (" << myRNA.get_RNA_length() << " nt)" << endl;
// load CSV file
if (access(motifs_path_name.c_str(), F_OK) == -1) {
cerr << "\033[31m" << motifs_path_name << " not found\033[0m" << endl;
return EXIT_FAILURE;
}
if (vm.count("jar3dcsv"))
posInsertionSites = load_csv(motifs_path_name.c_str());
else if (vm.count("bayespaircsv"))
posInsertionSites = load_csv(motifs_path_name.c_str());
else
posInsertionSites = load_desc_folder(motifs_path_name.c_str(), fa->seq(), verbose);
/* FIND PARETO SET */
MOIP myMOIP = MOIP(myRNA, posInsertionSites, theta_p_threshold, verbose);
double min, max;
IloConstraintArray F(myMOIP.get_env());
try {
bestSSO1 = myMOIP.solve_objective(1, -__DBL_MAX__, __DBL_MAX__);
bestSSO2 = myMOIP.solve_objective(2, -__DBL_MAX__, __DBL_MAX__);
if (verbose) {
cout << endl << "Best solution according to objective 1 :" << bestSSO1.to_string() << endl;
cout << "Best solution according to objective 2 :" << bestSSO2.to_string() << endl;
}
// extend the Pareto set on top
if (MOIP::obj_to_solve_ == 1) {
myMOIP.add_solution(bestSSO1);
min = bestSSO1.get_objective_score(2) + MOIP::precision_;
max = bestSSO2.get_objective_score(2);
if (verbose) cout << endl << "Solving obj1 on top of best solution 1." << endl;
} else {
myMOIP.add_solution(bestSSO2);
min = bestSSO2.get_objective_score(1) + MOIP::precision_;
max = bestSSO1.get_objective_score(1);
if (verbose) cout << endl << "Solving obj2 on top of best solution 2." << endl;
}
if (verbose)
cout << setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function " << MOIP::obj_to_solve_ << ", on top of "
<< min << ": Obj" << 3 - MOIP::obj_to_solve_ << " being in [" << min << ", " << max << "]..." << endl;
myMOIP.search_between(min, max);
// extend the Pareto set below
if (MOIP::obj_to_solve_ == 1) {
if (verbose) cout << endl << "Solving obj1 below best solution 1." << endl;
min = -__DBL_MAX__;
max = bestSSO1.get_objective_score(2);
} else {
if (verbose) cout << endl << "Solving obj2 below best solution 2." << endl;
min = -__DBL_MAX__;
max = bestSSO2.get_objective_score(1);
}
if (verbose)
cout << setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function " << MOIP::obj_to_solve_
<< ", below (or eq. to) " << max << ": Obj" << 3 - MOIP::obj_to_solve_ << " being in [" << min << ", "
<< max << "]..." << endl
<< "\t>forbidding " << F.getSize() << " solutions found in [" << setprecision(10)
<< min - MOIP::precision_ << ", " << max + MOIP::precision_ << ']' << endl;
myMOIP.search_between(min, max);
} catch (IloCplex::Exception& e) {
cerr << "\033[31mCplex Exception: " << e.getMessage() << "\033[0m" << endl;
exit(EXIT_FAILURE);
}
/* DISPLAY RESULTS */
// print the pareto set
if (verbose) {
cout << endl << endl << "---------------------------------------------------------------" << endl;
cout << "Whole Pareto Set:" << endl;
for (uint i = 0; i < myMOIP.get_n_solutions(); i++) myMOIP.solution(i).print();
cout << endl;
cout << posInsertionSites.size() << " candidate insertion sites, " << myMOIP.get_n_solutions() << " solutions kept." << endl;
cout << "Best value for Motif insertion objective: " << bestSSO1.get_objective_score(1) << endl;
cout << "Best value for structure expected accuracy: " << bestSSO2.get_objective_score(2) << endl;
}
// Save it to file
if (vm.count("output")) {
if (verbose) cout << "Saving structures to " << outputName << "..." << endl;
outfile.open(outputName);
outfile << fa->name() << endl << fa->seq() << endl;
for (uint i = 0; i < myMOIP.get_n_solutions(); i++) outfile << myMOIP.solution(i).to_string() << endl;
outfile.close();
}
/* QUIT */
return EXIT_SUCCESS;
}