Louis BECQUEY / biorseo

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Louis BECQUEY
d7ca4934 1 parent 8fb20871

Support for the old Rna3dMotif .desc format as input

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Showing 4 changed files with 82 additions and 45 deletions
......@@ -14,7 +14,7 @@ CXXFLAGS = --std=c++17 -Wall -Wpedantic -Wextra -Wno-ignored-attributes -Wno-unu
LINKER = clang++
# linking flags here
LDFLAGS = -L$(LCONCERT) -L$(LCPLEX) -lconcert -lilocplex -lcplex -lpthread -ldl -lnupackpfunc -lnupackutils
LDFLAGS = -L$(LCONCERT) -L$(LCPLEX) -lboost_system -lboost_filesystem -lconcert -lilocplex -lcplex -lpthread -ldl -lnupackpfunc -lnupackutils
# change these to proper directories where each file should be
SRCDIR = cppsrc
......
......@@ -22,7 +22,15 @@ struct recursive_directory_range {
Motif::Motif(void) {}
void Motif::build_from_desc(const string& descfile)
Motif::Motif(const vector<Component>& v, string PDB) : comp(v), PDBID(PDB)
{
is_model_ = false;
reversed_ = false;
source_ = RNA3DMOTIF;
}
vector<Motif> Motif::build_from_desc(const string& descfile, string rna)
{
std::ifstream motif;
string line;
......@@ -30,11 +38,7 @@ void Motif::build_from_desc(const string& descfile)
vector<string> component_sequences;
vector<string> bases;
int last;
PDBID = descfile.substr(0, descfile.find(".desc"));
is_model_ = false;
reversed_ = false;
source_ = RNA3DMOTIF;
vector<Motif> results;
motif = std::ifstream(descfile);
std::getline(motif, line); // ignore "id: number"
......@@ -49,25 +53,30 @@ void Motif::build_from_desc(const string& descfile)
if (pos - last > 5) { // finish this component and start a new one
component_sequences.push_back(seq);
seq = nt;
} else if (pos - last == 1) { // we are on the same component
seq += nt;
seq = "";
} else if (pos - last == 2) {
seq += '.' + nt;
seq += '.';
} else if (pos - last == 3) {
seq += ".." + nt;
seq += "..";
} else if (pos - last == 4) {
seq += "..." + nt;
seq += "...";
} else if (pos - last == 5) {
seq += "...." + nt;
seq += "....";
}
seq += nt;
}
// Now component_sequences is a vector of sequences like {AGCGC, CGU..GUUU}
for (string& comp : component_sequences) {
// We need to search for the different positions where to insert the first component
vector<vector<Component>> vresults = find_next_ones_in(rna, component_sequences);
// Now create proper motifs
for (vector<Component>& v : vresults) {
results.push_back(Motif(v, descfile.substr(0, descfile.find(".desc"))));
}
return results;
}
void Motif::load_from_csv(string csv_line)
{
vector<string> tokens;
......@@ -82,7 +91,6 @@ void Motif::load_from_csv(string csv_line)
source_ = RNAMOTIFATLAS;
}
string Motif::pos_string(void) const
{
std::stringstream s;
......@@ -100,12 +108,35 @@ string Motif::get_identifier(void) const
}
}
vector<vector<Component>> Motif::find_next_ones_in(string rna, vector<string> vc)
{
std::smatch matches;
std::regex c(vc[0]);
pair<uint, uint> pos;
vector<vector<Component>> results;
vector<vector<Component>> next_ones;
vector<string> next_seqs(&vc[1], &vc[vc.size() - 1]);
std::regex_search(rna, matches, c);
for (uint i = 0; i < matches.size(); ++i) // Pour chacun des matches
{
pos.first = matches.position(i);
pos.second = matches.length(i) + pos.first - 1;
next_ones = find_next_ones_in(rna.substr(pos.second + 1), next_seqs);
for (vector<Component> v : next_ones) // Pour chacune des combinaisons suivantes
{
// Combiner le match et la combinaison suivante
vector<Component> r;
r.push_back(Component(pos));
for (Component& c : v) r.push_back(c);
results.push_back(r);
}
}
return results;
}
vector<Motif> load_desc_folder(const string& path, const string& rna)
vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbose)
{
vector<Motif> posInsertionSites;
......@@ -115,9 +146,9 @@ vector<Motif> load_desc_folder(const string& path, const string& rna)
}
for (auto it : recursive_directory_range(path)) {
if (is_desc_insertible(it.path().string(), rna)) {
posInsertionSites.push_back(Motif());
posInsertionSites.back().build_from_desc(it.path().string());
if (is_desc_insertible(it.path().string(), rna, verbose)) {
vector<Motif> m = Motif::build_from_desc(it.path().string(), rna);
for (Motif& mot : m) posInsertionSites.push_back(mot);
}
}
return posInsertionSites;
......@@ -158,18 +189,17 @@ bool is_desc_insertible(const string& descfile, const string& rna, bool verbose)
int pos = std::stoi(b->substr(0, b->find('_')));
if (pos - last > 5) { // finish this component and start a new one
seq += ".{5,}" + nt;
} else if (pos - last == 1) { // we are on the same component
seq += nt;
seq += ".{5,}";
} else if (pos - last == 2) {
seq += "." + nt;
seq += ".";
} else if (pos - last == 3) {
seq += ".." + nt;
seq += "..";
} else if (pos - last == 4) {
seq += "..." + nt;
seq += "...";
} else if (pos - last == 5) {
seq += "...." + nt;
seq += "....";
}
seq += nt; // pos - last == 1 in particular
last = pos;
}
std::smatch m;
......
......@@ -13,32 +13,38 @@ typedef struct Comp_ {
size_t k;
string seq_;
Comp_(pair<int, int> p) : pos(p) { k = 1 + pos.second - pos.first; }
Comp_(uint start, uint length) : k(length)
{
pos.first = start;
pos.second = start + length - 1;
}
} Component;
class Motif
{
public:
Motif();
void load_from_csv(string csv_line);
void build_from_desc(const string& descfile);
string pos_string(void) const;
string get_origin(void) const;
string get_identifier(void) const;
vector<Component> comp;
double score_;
bool reversed_;
Motif(const vector<Component>& v, string PDB);
void load_from_csv(string csv_line);
static vector<Motif> build_from_desc(const string& descfile, string rna);
string pos_string(void) const;
string get_origin(void) const;
string get_identifier(void) const;
vector<Component> comp;
double score_;
bool reversed_;
private:
static vector<vector<Component>> find_next_ones_in(string rna, vector<string> vc);
string atlas_id; // if source = RNAMOTIFATLAS
string PDBID; // if source = RNA3DMOTIF
bool is_model_; // Wether the motif is a model or an extracted module from a 3D structure
enum { RNA3DMOTIF = 1, RNAMOTIFATLAS = 2, CARNAVAL = 3 } source_;
};
bool is_desc_insertible(const string& descfile, const string& rna);
vector<Motif> load_desc_folder(const string& path);
bool is_desc_insertible(const string& descfile, const string& rna, bool verbose);
vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbose);
vector<Motif> load_jar3d_output(const string& path);
// utilities to compare secondary structures:
......
......@@ -93,9 +93,10 @@ int main(int argc, char* argv[])
cerr << csvname << " not found" << endl;
return EXIT_FAILURE;
}
posInsertionSites = load_desc_folder(csvname);
posInsertionSites = load_desc_folder(csvname, fa->seq(), verbose);
if (verbose)
cout << "\t>" << csvname << " successfuly loaded (" << posInsertionSites.size() << " insertion sites)" << endl;
exit(0);
/* FIND PARETO SET */
......