Motif.cpp
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#include "Motif.h"
#include "Pool.h"
#include <boost/algorithm/string.hpp>
#include <iostream>
#include <regex>
#include <sstream>
#include <thread>
#include <json.hpp>
using namespace boost::filesystem;
using namespace std;
using json = nlohmann::json;
Motif::Motif(void) {}
Motif::Motif(const vector<Component>& v, string PDB) : comp(v), PDBID(PDB)
{
is_model_ = false;
reversed_ = false;
source_ = RNA3DMOTIF;
}
Motif::Motif(const vector<Component>& v, string id, size_t nb_contacts, double tx_occurrences) : comp(v)
{
contacts_id = id;
is_model_ = false;
reversed_ = false;
source_ = CONTACTS;
contact_ = nb_contacts;
tx_occurrences_ = tx_occurrences;
}
Motif::Motif(string csv_line)
{
vector<string> tokens;
split(tokens, csv_line, boost::is_any_of(","));
if (csv_line.find(string("True")) != std::string::npos or csv_line.find(string("False")) != std::string::npos) // This has been created by jar3d
{
atlas_id = tokens[0];
score_ = stoi(tokens[2]);
comp.push_back(Component(make_pair<int, int>(stoi(tokens[3]), stoi(tokens[4]))));
if (tokens[5] != "-") comp.push_back(Component(make_pair<int, int>(stoi(tokens[5]), stoi(tokens[6]))));
reversed_ = (tokens[1] == "True");
is_model_ = true;
PDBID = "";
source_ = RNAMOTIFATLAS;
}
else // this has been created by BayesPairing
{
score_ = stoi(tokens[1]);
// identify source:
if (tokens[0].find(string("rna3dmotif")) == std::string::npos)
{
is_model_ = true;
PDBID = "";
source_ = RNAMOTIFATLAS;
atlas_id = tokens[0];
}
else
{
is_model_ = false;
PDBID = tokens[0];
source_ = RNA3DMOTIF;
atlas_id = "";
}
uint i = 2;
//while (i < tokens.size())
while (i < tokens.size()-1)
{
if (stoi(tokens[i]) < stoi(tokens[i + 1]))
comp.push_back(Component(make_pair<int, int>(stoi(tokens[i]), stoi(tokens[i + 1]))));
else
i = i + 0;
i += 2;
}
}
}
Motif::Motif(const vector<Component>& v, path rinfile, uint id, bool reversed) : comp(v), reversed_(reversed)
{
// Loads a motif from the RIN file of Carnaval
carnaval_id = to_string(id);
source_ = CARNAVAL;
is_model_ = false;
std::ifstream file(rinfile);
if (file.is_open())
{
string line;
getline(file,line); //skip the header_link line
getline(file,line); //get the links line
string link_str;
size_t index = 0;
string nt_str;
size_t sub_index = 0;
while (line != "")
{
Link link;
//link.nts
index = line.find(";");
link_str = line.substr(0, index);
line.erase(0, index+1);
sub_index = link_str.find(",");
nt_str = link_str.substr(0, sub_index);
link_str.erase(0, sub_index+1);
link.nts.first = stoi(nt_str);
sub_index = link_str.find(",");
nt_str = link_str.substr(0, sub_index);
link_str.erase(0, sub_index+1);
link.nts.second = stoi(nt_str);
//link.long_range
link.long_range = (link_str == "True");
links_.push_back(link);
}
// Now renumber the Links based on the components positions.
for (Link& l : links_) {
size_t sum_comp = 0;
size_t j;
for (j=0; j<v.size(); j++) {
const Component& c = v[j];
if (l.nts.first >= sum_comp and l.nts.first < sum_comp + c.k) {
// This is the right component
l.nts.first += c.pos.first - sum_comp;
sum_comp += c.k;
break;
}
sum_comp += c.k;
}
for (; j<v.size(); j++) {
const Component& c = v[j];
if (l.nts.second >= sum_comp and l.nts.second < sum_comp + c.k) {
// This is the right component
l.nts.second += c.pos.second - sum_comp;
break;
}
sum_comp += c.k;
}
}
}
else cout << "\t> RIN file not found : " << rinfile << endl;
}
string Motif::pos_string(void) const
{
stringstream s;
s << atlas_id << " ( ";
for (auto c : comp) s << c.pos.first << '-' << c.pos.second << ' ';
s << ')';
return s.str();
}
string Motif::sec_struct(void) const
{
// Fill a string of the right size with dots
string secstruct = string("");
secstruct += to_string(comp.size()) + string(" components: ");
for (auto c : comp) {
for (uint k = c.pos.first; k<=c.pos.second; k++) secstruct += ".";
secstruct += " ";
}
// Replace dots by brackets
secstruct += "basepairs:";
for (auto l : links_) {
secstruct += '\t' + to_string(l.nts.first) + '-' + to_string(l.nts.second);
}
return secstruct;
}
string Motif::get_identifier(void) const
{
switch (source_) {
case RNAMOTIFATLAS: return atlas_id; break;
case CARNAVAL: return string("RIN") + carnaval_id; break;
case CONTACTS: return string("JSON") + contacts_id; break;
default: return PDBID;
}
}
char Motif::is_valid_DESC(const string& descfile)
{
// /!\ returns 0 if no errors
std::ifstream motif;
string line;
vector<string> bases;
char c = 'a';
char* prev = &c;
motif = std::ifstream(descfile);
getline(motif, line); // ignore "id: number"
getline(motif, line); // Bases: 866_G 867_G 868_G 869_G 870_U 871_A ...
boost::split(bases, line, [prev](char c) {
bool res = (*prev == ' ' or *prev == ':');
*prev = c;
return (c == ' ' and res);
}); // get a vector of 866_G, 867_G, etc...
for (vector<string>::iterator b = (bases.begin() + 1); b != (bases.end() - 1); b++) {
char nt = b->substr(b->find('_') + 1, 1).back();
int pos = stoi(b->substr(0, b->find('_')));
if (string(1, nt).find_first_not_of("ACGU") != string::npos) return nt;
if (pos <= 0) return '-';
}
while (getline(motif, line)) {
uint slash = line.find('/');
string interaction(line.substr(slash - 1, 3));
string b1 = line.substr(line.find('(') + 1, 8); // The first base (position_nucleotide)
string temp = line.substr(slash + 1);
string b2 = temp.substr(temp.find('(') + 1, 8); // The second base (position_nucleotide)
b1.erase(remove(b1.begin(), b1.end(), ' '), b1.end());
b2.erase(remove(b2.begin(), b2.end(), ' '), b2.end());
int p1 = stoi(b1.substr(0, b1.find('_')));
int p2 = stoi(b2.substr(0, b2.find('_')));
if ((p2 - p1 != 1) and !interaction.compare("C/C")) return 'b';
if ((p2 - p1 < 4) and (!interaction.compare("+/+") or !interaction.compare("-/-"))) return 'l';
}
return 0;
}
char Motif::is_valid_RIN(const string& rinfile)
{
string line;
uint n_basepairs, index, motif_length = 0;
std::ifstream motif = std::ifstream(rinfile);
getline(motif, line); //skip the header_link line
getline(motif, line); //get the links line
n_basepairs = count_if(line.begin(), line.end(), [](char c){ return (c==';'); });
getline(motif, line); //skip the header_comp line
while (getline(motif, line))
{
// components are formatted like:
// pos;k;seq (position, length, sequence)
// 0,1;2;GU
if (line == "\n") break; //skip last line (empty)
size_t start = line.find(";") + 1;
index = line.find(";", start); // find the second ';'
motif_length += stoi(line.substr(line.find(";")+1, index));
}
if (motif_length < 5) return 'l';
if (!n_basepairs) return 'x';
return (char) 0;
}
vector<pair<uint,char>> Motif::is_valid_JSON(const string& jsonfile)
{
// returns 0 if no errors
std::ifstream motif;
motif = std::ifstream(jsonfile);
json js = json::parse(motif);
vector<pair<uint,char>> errors_id;
vector<string> components;
uint fin = 0;
std::string keys[6] = {"contacts", "occurences", "pdb", "pfam", "sequence", "struct2d"};
// Iterating over Motifs
for (auto i = js.begin(); i != js.end(); ++i) {
int j = 0;
string id = i.key();
size_t size;
string complete_seq;
string contacts;
// Iterating over json keys
for (auto it = js[id].begin(); it != js[id].end(); ++it) {
// it.key() contains the key, and it.value() the field's value.
string curr_key = it.key();
if (curr_key.compare(keys[j]))
{
//std::cout << "error header : keys[" << j << "]: " << keys[j] << " vs curr_key: " << curr_key << endl;
errors_id.push_back(make_pair(stoi(id), 'd'));
//return 'd';
}
else if(!curr_key.compare(keys[5])) // This is the secondary structure field
{
string ss = it.value();
if (ss.empty()) {
errors_id.push_back(make_pair(stoi(id), 'f'));
break;
} else if (!checkSecondaryStructure(ss)) {
errors_id.push_back(make_pair(stoi(id), 'n'));
break;
} else if (ss.size() != complete_seq.size()) {
errors_id.push_back(make_pair(stoi(id), 'x'));
break;
}
}
else if(!curr_key.compare(keys[0])) // This is the contacts field
{
contacts = it.value();
}
else if (!curr_key.compare(keys[4])) // This is the sequence field
{
string seq = it.value();
size = count_nucleotide(seq);
complete_seq = seq;
if (seq.empty()) {
errors_id.push_back(make_pair(stoi(id), 'e'));
break;
}
if (size < 4) {
errors_id.push_back(make_pair(stoi(id), 'l'));
break;
}
size_t count_contact = count_delimiter(contacts);
size_t count_seq = count_delimiter(seq);
if (count_contact != count_seq) {
errors_id.push_back(make_pair(stoi(id), 'a'));
break;
}
if (contacts.size() != seq.size()) {
errors_id.push_back(make_pair(stoi(id), 'b'));
break;
}
// Iterate on components to check their length
string subseq;
while((seq.find('&') != string::npos)) {
fin = seq.find('&');
subseq = seq.substr(0, fin);
seq = seq.substr(fin + 1);
if (subseq.size() >= 2) {
components.push_back(subseq);
} else {
//errors_id.push_back(make_pair(stoi(id), 'k'));
}
}
if (seq.size() >= 2) { // Last component after the last &
components.push_back(seq);
} else {
//errors_id.push_back(make_pair(stoi(id), 'k'));
}
size_t n = 0;
for (uint ii = 0; ii < components.size(); ii++) {
n += components[ii].size();
}
if(n <= 3) {
errors_id.push_back(make_pair(stoi(id), 'l'));
}
}
j++;
}
}
return errors_id;
}
//count the number of nucleotide in the motif sequence
size_t count_nucleotide(string& seq) {
size_t count = 0;
for(uint i = 0; i < seq.size(); i++) {
char c = seq.at(i);
if (c != '&') {
count++;
}
}
return count;
}
//count the number of '&' in the motif sequence
size_t count_delimiter(string& seq) {
size_t count = 0;
for(uint i = 0; i < seq.size(); i++) {
char c = seq.at(i);
if (c == '&') {
count++;
}
}
return count;
}
//count the number of '*' in the motif
size_t count_contacts(string& contacts) {
size_t count = 0;
for (uint i = 0; i < contacts.size(); i++) {
if (contacts[i] == '*') {
count++;
}
}
return count;
}
//Check if the sequence is a rna sequence (ATGC) and replace T by U or remove modified nucleotide if necessary
string check_motif_sequence(string seq) {
std::transform(seq.begin(), seq.end(), seq.begin(), ::toupper);
for (int i = seq.size(); i >= 0; i--) {
if(seq[i] == 'T') {
seq[i] = 'U';
} else if (!(seq [i] == 'A' || seq [i] == 'U' || seq [i] == '&'
|| seq [i] == 'G' || seq [i] == 'C')) {
seq = seq.erase(i,1);
}
}
return seq;
}
//check that there are as many opening parentheses as closing ones
bool checkSecondaryStructure(string struc)
{
stack<uint> parentheses;
stack<uint> crochets;
stack<uint> accolades;
stack<uint> chevrons;
for (uint i = 0; i < struc.length(); i++)
{
if (struc[i] != '(' && struc[i] != ')'
&& struc[i] != '.' && struc[i] != '&'
&& struc[i] != '[' && struc[i] != ']'
&& struc[i] != '{' && struc[i] != '}'
&& struc[i] != '<' && struc[i] != '>') {
return false;
} else {
for (uint i = 0; i < struc.size(); i++) {
if (struc[i] == '(') {
parentheses.push(i);
} else if (struc[i] == ')') {
if (!parentheses.empty())
parentheses.pop();
else return false;
} else if (struc[i] == '[') {
crochets.push(i);
} else if (struc[i] == ']') {
if (!crochets.empty())
crochets.pop();
else return false;
} else if (struc[i] == '{') {
accolades.push(i);
} else if (struc[i] == '}') {
if (!accolades.empty())
accolades.pop();
else return false;
} else if (struc[i] == '<') {
chevrons.push(i);
} else if (struc[i] == '>') {
if (!chevrons.empty())
chevrons.pop();
else return false;
}
}
}
}
return (parentheses.empty() && crochets.empty() && accolades.empty() && chevrons.empty());
}
// Converts a dot-bracket motif secondary structure to vector of Link
vector<Link> build_motif_pairs(string& struc, vector<Component>& v) {
vector<Link> vec;
stack<uint> parentheses;
stack<uint> crochets;
stack<uint> accolades;
stack<uint> chevrons;
uint count = 0;
uint debut = v[count].pos.first;
uint gap = 0;
for (uint i = 0; i < struc.size(); i++) {
if (struc[i] == '(') {
parentheses.push(i + debut + gap - count);
} else if (struc[i] == ')') {
Link l;
l.nts.first = parentheses.top();
l.nts.second = i + debut + gap - count;
vec.push_back(l);
parentheses.pop();
} else if (struc[i] == '[') {
crochets.push(i + debut + gap - count);
} else if (struc[i] == ']') {
Link l;
l.nts.first = crochets.top();
l.nts.second = i + debut + gap - count;
vec.push_back(l);
crochets.pop();
} else if (struc[i] == '{') {
accolades.push(i + debut + gap - count);
} else if (struc[i] == '}') {
Link l;
l.nts.first = accolades.top();
l.nts.second = i + debut + gap - count;
vec.push_back(l);
accolades.pop();
} else if (struc[i] == '<') {
chevrons.push(i + debut + gap - count);
} else if (struc[i] == '>') {
Link l;
l.nts.first = chevrons.top();
l.nts.second = i + debut + gap - count;
vec.push_back(l);
chevrons.pop();
} else if (struc[i] == '&') {
count ++;
gap += v[count].pos.first - v[count - 1].pos.second - 1;
}
}
return vec;
}
uint find_max_occurrences(string& filepath) {
uint max = 0;
std::ifstream in = std::ifstream(filepath);
json js = json::parse(in);
string contacts_id;
for(auto it = js.begin(); it != js.end(); ++it) {
contacts_id = it.key();
for(auto it2 = js[contacts_id].begin(); it2 != js[contacts_id].end(); ++it2) {
string test = it2.key();
if (!test.compare("occurences")) {
uint occ = it2.value();
if (occ > max) {
max = occ;
}
}
}
}
return max;
}
uint find_max_sequence(string& filepath) {
uint max = 0;
std::ifstream in = std::ifstream(filepath);
json js = json::parse(in);
string contacts_id;
string seq;
for(auto it = js.begin(); it != js.end(); ++it) {
contacts_id = it.key();
for(auto it2 = js[contacts_id].begin(); it2 != js[contacts_id].end(); ++it2) {
string test = it2.key();
if (!test.compare("sequence")) {
seq = it2.value();
uint size = seq.size();
if (size > max) {
max = size;
}
}
}
}
return max;
}
vector<string> find_components(string& sequence, string delimiter) {
vector<string> list;
string seq = sequence;
string subseq;
uint fin = 0;
while(seq.find(delimiter) != string::npos) {
fin = seq.find(delimiter);
subseq = seq.substr(0, fin);
seq = seq.substr(fin + 1);
list.push_back(subseq); // new component sequence
}
if (!seq.empty()) {
list.push_back(seq);
}
return list;
}
vector<uint> find_contacts(vector<string>& struc2d, vector<Component>& v) {
vector<uint> positions;
string delimiter = "*";
uint debut;
for (uint i = 0; i < v.size(); i++) {
debut = v[i].pos.first;
uint pos = struc2d[i].find(delimiter, 0);
while(pos != string::npos && pos <= struc2d[i].size())
{
positions.push_back(pos + debut);
pos = struc2d[i].find(delimiter, pos+1);
}
}
return positions;
}
bool is_desc_insertible(const string& descfile, const string& rna)
{
std::ifstream motif;
string line;
string seq;
vector<string> bases;
int last;
char c = 'a';
char* prev = &c;
motif = std::ifstream(descfile);
getline(motif, line); // ignore "id: number"
getline(motif, line); // Bases: 866_G 867_G 868_G 869_G 870_U 871_A ...
boost::split(bases, line, [prev](char c) {
bool res = (*prev == ' ' or *prev == ':');
*prev = c;
return (c == ' ' and res);
}); // get a vector of 866_G, 867_G, etc...
seq = "";
last = stoi(bases[1].substr(0, bases[1].find('_')));
for (vector<string>::iterator b = (bases.begin() + 1); b != (bases.end() - 1); b++) {
char nt = b->substr(b->find('_') + 1, 1).back();
int pos = stoi(b->substr(0, b->find('_')));
if (pos - last > 5) { // finish this component and start a new one
seq += ".{5,}";
} else if (pos - last == 2) {
seq += ".";
} else if (pos - last == 3) {
seq += "..";
} else if (pos - last == 4) {
seq += "...";
} else if (pos - last == 5) {
seq += "....";
}
seq += nt; // pos - last == 1 in particular
last = pos;
}
smatch m;
regex e(seq);
return regex_search(rna, m, e);
}
vector<vector<Component>> find_next_ones_in(string rna, uint offset, vector<string>& vc)
{
pair<uint, uint> pos;
vector<vector<Component>> results;
vector<vector<Component>> next_ones;
vector<string> next_seqs;
regex c(vc[0]);
//cout << "\t\t>Searching " << vc[0] << " in " << rna << endl;
if (vc.size() > 1) {
//cout << "size vc: " << vc.sizef() << endl;
if (regex_search(rna, c)) {
if (vc.size() > 2) {
next_seqs = vector<string>(&vc[1], &vc[vc.size()]);
}
else {
next_seqs = vector<string>(1, vc.back());
}
uint j = 0;
// For every regexp match
for (sregex_iterator i = sregex_iterator(rna.begin(), rna.end(), c); i != sregex_iterator(); ++i) {
smatch match = *i;
pos.first = match.position() + offset;
pos.second = pos.first + match.length() - 1;
//cout << "\t\t>Inserting " << vc[j] << " in [" << pos.first << ',' << pos.second << "]" << endl;
// +5 because HL < 3 pbs but not for CaRNAval or Contacts
// if CaRNAval or Contacts +2 is better
if (pos.second - offset + 5 >= rna.length()) {
//cout << "\t\t... but we cannot place the next components : Ignored." << endl;
continue;
}
next_ones = find_next_ones_in(rna.substr(pos.second - offset + 5), pos.second + 5, next_seqs);
if (!next_ones.size()) {
// cout << "\t\t... but we cannot place the next components : Ignored.2" << endl;
continue;
}
//cout << endl;
for (vector<Component> v : next_ones) // For every combination of the next components
{
// Combine the match for this component pos with the combination
// of next_ones as a whole solution
vector<Component> r;
r.push_back(Component(pos));
for (Component& c : v) r.push_back(c);
results.push_back(r);
}
j++;
}
}
} else {
// Only one more component to find
if (regex_search(rna, c)) {
// For each regexp match
for (sregex_iterator i = sregex_iterator(rna.begin(), rna.end(), c); i != sregex_iterator(); ++i) {
smatch match = *i;
pos.first = match.position() + offset;
pos.second = pos.first + match.length() - 1;
//cout << "\t\t>Inserting " << vc[0] << " in [" << pos.first << ',' << pos.second << "]" << endl;
// Create a vector of component with one component for that match
vector<Component> r;
r.push_back(Component(pos));
results.push_back(r);
}
}
}
return results;
}
vector<vector<Component>> json_find_next_ones_in(string rna, uint offset, vector<string>& vc)
{
pair<uint, uint> pos;
vector<vector<Component>> results;
vector<vector<Component>> next_ones;
vector<string> next_seqs;
regex c(vc[0]);
//cout << "\t\t>Searching " << vc[0] << " in " << rna << endl;
if (vc.size() > 1) {
//cout << "size vc: " << vc.size() << endl;
if (regex_search(rna, c)) {
if (vc.size() > 2) {
next_seqs = vector<string>(&vc[1], &vc[vc.size()]);
}
else {
next_seqs = vector<string>(1, vc.back());
}
uint j = 0;
// For every regexp match
for (sregex_iterator i = sregex_iterator(rna.begin(), rna.end(), c); i != sregex_iterator(); ++i) {
smatch match = *i;
pos.first = match.position() + offset;
pos.second = pos.first + match.length() - 1;
//cout << "\t\t>Inserting " << vc[j] << " in [" << pos.first << ',' << pos.second << "]" << endl;
// +5 because HL < 3 pbs but not for CaRNAval or Contacts
// if CaRNAval or Contacts +2 is better
if (pos.second - offset + 2 >= rna.length()) {
//cout << "\t\t... but we cannot place the next components : Ignored." << endl;
continue;
}
next_ones = json_find_next_ones_in(rna.substr(pos.second - offset + 2), pos.second + 2, next_seqs);
if (!next_ones.size()) {
// cout << "\t\t... but we cannot place the next components : Ignored.2" << endl;
continue;
}
//cout << endl;
for (vector<Component> v : next_ones) // For every combination of the next components
{
// Combine the match for this component pos with the combination
// of next_ones as a whole solution
vector<Component> r;
r.push_back(Component(pos));
for (Component& c : v) r.push_back(c);
results.push_back(r);
}
j++;
}
}
} else {
// Only one more component to find
if (regex_search(rna, c)) {
// For each regexp match
for (sregex_iterator i = sregex_iterator(rna.begin(), rna.end(), c); i != sregex_iterator(); ++i) {
smatch match = *i;
pos.first = match.position() + offset;
pos.second = pos.first + match.length() - 1;
//cout << "\t\t>Inserting " << vc[0] << " in [" << pos.first << ',' << pos.second << "]" << endl;
// Create a vector of component with one component for that match
vector<Component> r;
r.push_back(Component(pos));
results.push_back(r);
}
}
}
return results;
}
bool operator==(const Component& c1, const Component& c2)
{
if (c1.pos.first != c2.pos.first) return false;
if (c1.pos.second != c2.pos.second) return false;
return true;
}
bool operator!=(const Component& c1, const Component& c2) { return not(c1 == c2); }
bool operator==(const Motif& m1, const Motif& m2)
{
if (m1.get_identifier() != m2.get_identifier()) return false;
if (m1.score_ != m2.score_) return false;
if (m1.reversed_ != m2.reversed_) return false;
for (uint i = 0; i < m1.comp.size(); i++)
if (m1.comp[i] != m2.comp[i]) return false;
return true;
}
bool operator!=(const Motif& m1, const Motif& m2) { return not(m1 == m2); }