extract_user_ct.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"
// Check if a vector of string are integers >= 1 and <= l
bool checkBasePairIndex(std::vector < std::string > v, uint l) {
bool res = true;
int e;
for(size_t i = 0, size = v.size(); i != size and res; i++) {
try {
e = std::stoi(v[i]);
if (e < 1 or e > int(l)) {
res = false;
}
} catch (std::string e) {
throw(e);
}
}
return res;
}
// Check if a vector of string are integers >= 0 and <= l
bool checkIndex(std::vector < std::string > v, uint l) {
bool res = true;
int e;
for(size_t i = 0, size = v.size(); i != size and res; i++) {
try {
e = std::stoi(v[i]);
if (e < 0 or e > l)
res = false;
} catch (std::string e) {
throw (e);
}
}
return res;
}
// Check if a vector of string are integers >= 0 and <= l -2
bool checkLength(std::vector < std::string > v, uint l) {
bool res = true;
int e;
for(size_t i = 0, size = v.size(); i != size and res; i++) {
try {
e = std::stoi(v[i]);
if (e < 0 or e > l-2)
res = false;
} catch (std::string e) {
throw (e);
}
}
return res;
}
// Add helix to ctHelix
void addHelix(int rna1, int rna2, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Helix * >& ctHelix,
std::string CTfile, int nLine) {
int i, j, ibis, jbis, l1;
try {
if (rna1 != rna2 and int(ctElements.size()) >= 9) { // Name1 \s Name2 \s IDmotif \s i \s i' \s j' \s j \s length \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[3], ctElements[4]}, rnaList_[rna1].get_n_())
and checkIndex({ctElements[5], ctElements[6]}, rnaList_[rna2].get_n_())
and checkLength({ctElements[7]}, rnaList_[rna1].get_n_())
and checkLength({ctElements[7]}, rnaList_[rna2].get_n_())
and checkIC(ctElements[8])) {
i = std::stoi(ctElements[3]);
ibis = std::stoi(ctElements[4]);
jbis = std::stoi(ctElements[5]);
j = std::stoi(ctElements[6]);
l1 = std::stoi(ctElements[7]);
if (i < ibis and jbis < j) {
// there is an helix with no information
if(i == 0 and j == 0 and ibis == 0 and jbis == 0 and l1 == 0)
ctHelix.push_back(new Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_(), std::stoi(ctElements[8])));
else {
if (l1 != 0 and i != 0)
ibis = i+l1-1;
if (l1 != 0 and ibis != 0)
i = ibis-l1+1;
if (l1 != 0 and jbis != 0)
j = jbis+l1-1;
if (l1 != 0 and j != 0)
jbis = j-l1+1;
if (i != 0 and ibis != 0)
l1 = ibis-i+1;
if (jbis != 0 and j != 0)
l1 = j-jbis+1;
// there is an helix with all information
if(i != 0 and j != 0 and ibis != 0 and jbis != 0 and l1 != 0)
ctHelix.push_back(new Helix(int(rna1), int(rna2), i-1, ibis-1, j-1, jbis-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_(), std::stoi(ctElements[8])));
// there is an helix with length information
else if (l1 != 0)
ctHelix.push_back(new Helix(int(rna1), int(rna2), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_(), std::stoi(ctElements[8])));
else
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
}
} else {
throw (std::string("Rules i < i' and j' < j are not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else if (rna1 == rna2 and int(ctElements.size()) >= 8) { // Name1 \space IDmotif \space i \s i' \s j' \s j \s length \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[2], ctElements[3], ctElements[4], ctElements[5]},
rnaList_[rna1].get_n_())
and checkLength({ctElements[6]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[7])) {
i = std::stoi(ctElements[2]);
ibis = std::stoi(ctElements[3]);
jbis = std::stoi(ctElements[4]);
j = std::stoi(ctElements[5]);
l1 = std::stoi(ctElements[6]);
if (i < ibis and ibis < jbis and jbis < j) {
// there is an helix with no information
if(i == 0 and j == 0 and ibis == 0 and jbis == 0 and l1 == 0)
ctHelix.push_back(new Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_(), std::stoi(ctElements[7])));
else {
if (l1 != 0 and i != 0)
ibis = i+l1-1;
if (l1 != 0 and ibis != 0)
i = ibis-l1+1;
if (l1 != 0 and jbis != 0)
j = jbis+l1-1;
if (l1 != 0 and j != 0)
jbis = j-l1+1;
if (i != 0 and ibis != 0)
l1 = ibis-i+1;
if (jbis != 0 and j != 0)
l1 = j-jbis+1;
// there is an helix with all information
if(i != 0 and j != 0 and ibis != 0 and jbis != 0 and l1 != 0)
ctHelix.push_back(new Helix(int(rna1), int(rna1), i-1, ibis-1, j-1, jbis-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_(), std::stoi(ctElements[7])));
// there is an helix with length information
else if (l1 != 0)
ctHelix.push_back(new Helix(int(rna1), int(rna1), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_(), std::stoi(ctElements[7])));
else {
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
}
}
} else {
throw (std::string("Rules i < i' and i' <j' and j' < j are not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in constraint file " + CTfile + ", line " + std::to_string(nLine) + ".\n" + e));
}
}
// Add pseudoknot to ctPseudo
void addPseudo(int rna1, int rna2, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Pseudoknot * >& ctPseudo,
std::string CTfile, int nLine) {
int i1, j1, ibis1, jbis1, i2, j2, ibis2, jbis2, l1, l2;
try {
if (rna1 != rna2 and int(ctElements.size()) >= 14) {
// Name1 \s Name2 \s IDmotif \s i1 \s i1' \s j1' \s j1 \s i2 \s i2' \s j2' \s j2 \s length1 \s length2 \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[3], ctElements[4], ctElements[7], ctElements[8]}, rnaList_[rna1].get_n_())
and checkIndex({ctElements[5], ctElements[6], ctElements[9], ctElements[10]}, rnaList_[rna2].get_n_())
and checkLength({ctElements[11]}, rnaList_[rna1].get_n_())
and checkLength({ctElements[12]}, rnaList_[rna2].get_n_())
and checkIC(ctElements[13])) {
i1 = std::stoi(ctElements[3]);
ibis1 = std::stoi(ctElements[4]);
jbis1 = std::stoi(ctElements[5]);
j1 = std::stoi(ctElements[6]);
i2 = std::stoi(ctElements[7]);
ibis2 = std::stoi(ctElements[8]);
jbis2 = std::stoi(ctElements[9]);
j2 = std::stoi(ctElements[10]);
l1 = std::stoi(ctElements[11]);
l2 = std::stoi(ctElements[12]);
if (i1 < ibis1 and jbis1 < j1 and i2 < ibis2 and jbis2 < j2) {
// there is a pseudoknot with no information
if(i1 == 0 and j1 == 0 and ibis1 == 0 and jbis1 == 0 and l1 == 0
and i2 == 0 and j2 == 0 and ibis2 == 0 and jbis2 == 0 and l2 == 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
else {
// Complete first helix
if (l1 != 0 and i1 != 0)
ibis1 = i1+l1-1;
if (l1 != 0 and ibis1 != 0)
i1 = ibis1-l1+1;
if (l1 != 0 and jbis1 != 0)
j1 = jbis1+l1-1;
if (l1 != 0 and j1 != 0)
jbis1 = j1-l1+1;
if (i1 != 0 and ibis1 != 0)
l1 = ibis1-i1+1;
if (jbis1 != 0 and j1 != 0)
l1 = j1-jbis1+1;
// Complete second helix
if (l2 != 0 and i2 != 0)
ibis2 = i2+l2-1;
if (l2 != 0 and ibis2 != 0)
i2 = ibis2-l2+1;
if (l2 != 0 and jbis2 != 0)
j2 = jbis2+l2-1;
if (l2 != 0 and j2 != 0)
jbis2 = j2-l2+1;
if (i2 != 0 and ibis2 != 0)
l2 = ibis2-i2+1;
if (jbis2 != 0 and j2 != 0)
l2 = j2-jbis2+1;
// there are two helices with all information
if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 != 0 and j2 != 0 and ibis2 != 0 and jbis2 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), i1-1, ibis1-1, j1-1, jbis1-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), i2-1, ibis2-1, j2-1, jbis2-1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
// the first helix is full
else if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 == 0 and j2 == 0 and ibis2 == 0 and jbis2 == 0 and l2 == 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), i1-1, ibis1-1, j1-1, jbis1-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
// the second helix is full
else if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 != 0 and j2 != 0 and ibis2 != 0 and jbis2 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), i2-1, ibis2-1, j2-1, jbis2-1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
// there are length information
else if (l1 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
else if (l1 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
else if (l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna2),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
Helix(int(rna1), int(rna2), -1, -1, -1, -1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna2].get_seq_()),
std::stoi(ctElements[13])));
else
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
}
} else {
throw (std::string("Rules i1 < i1' and j1' < j1 and i2 < i2' and j2' < j2 are not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else if (rna1 == rna2 and int(ctElements.size()) >= 13) {
// Name1 \s IDmotif \s i1 \s i1' \s j1' \s j1 \s i2 \s i2' \s j2' \s j2 \s length1 \s length2 \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[2], ctElements[3], ctElements[6], ctElements[7]}, rnaList_[rna1].get_n_())
and checkIndex({ctElements[4], ctElements[5], ctElements[8], ctElements[9]}, rnaList_[rna1].get_n_())
and checkLength({ctElements[10]}, rnaList_[rna1].get_n_())
and checkLength({ctElements[11]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[12])) {
i1 = std::stoi(ctElements[2]);
ibis1 = std::stoi(ctElements[3]);
jbis1 = std::stoi(ctElements[4]);
j1 = std::stoi(ctElements[5]);
i2 = std::stoi(ctElements[6]);
ibis2 = std::stoi(ctElements[7]);
jbis2 = std::stoi(ctElements[8]);
j2 = std::stoi(ctElements[9]);
l1 = std::stoi(ctElements[10]);
l2 = std::stoi(ctElements[11]);
if (i1 < ibis1 and jbis1 < j1 and i2 < ibis2 and jbis2 < j2) {
// there is a pseudoknot with no information
if(i1 == 0 and j1 == 0 and ibis1 == 0 and jbis1 == 0 and l1 == 0
and i2 == 0 and j2 == 0 and ibis2 == 0 and jbis2 == 0 and l2 == 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
else {
// Complete first helix
if (l1 != 0 and i1 != 0)
ibis1 = i1+l1-1;
if (l1 != 0 and ibis1 != 0)
i1 = ibis1-l1+1;
if (l1 != 0 and jbis1 != 0)
j1 = jbis1+l1-1;
if (l1 != 0 and j1 != 0)
jbis1 = j1-l1+1;
if (i1 != 0 and ibis1 != 0)
l1 = ibis1-i1+1;
if (jbis1 != 0 and j1 != 0)
l1 = j1-jbis1+1;
// Complete second helix
if (l2 != 0 and i2 != 0)
ibis2 = i2+l2-1;
if (l2 != 0 and ibis2 != 0)
i2 = ibis2-l2+1;
if (l2 != 0 and jbis2 != 0)
j2 = jbis2+l2-1;
if (l2 != 0 and j2 != 0)
jbis2 = j2-l2+1;
if (i2 != 0 and ibis2 != 0)
l2 = ibis2-i2+1;
if (jbis2 != 0 and j2 != 0)
l2 = j2-jbis2+1;
// there are two helices with all information
if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 != 0 and j2 != 0 and ibis2 != 0 and jbis2 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), i1-1, ibis1-1, j1-1, jbis1-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), i2-1, ibis2-1, j2-1, jbis2-1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
// the first helix is full
else if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 == 0 and j2 == 0 and ibis2 == 0 and jbis2 == 0 and l2 == 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), i1-1, ibis1-1, j1-1, jbis1-1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
// the second helix is full
else if(i1 != 0 and j1 != 0 and ibis1 != 0 and jbis1 != 0 and l1 != 0
and i2 != 0 and j2 != 0 and ibis2 != 0 and jbis2 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), i2-1, ibis2-1, j2-1, jbis2-1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
// there are length information
else if (l1 != 0 and l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
else if (l1 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, l1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
else if (l2 != 0)
ctPseudo.push_back(new Pseudoknot(int(rna1), int(rna1),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, -1,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
Helix(int(rna1), int(rna1), -1, -1, -1, -1, l2,
rnaList_[rna1].get_seq_(), rnaList_[rna1].get_seq_()),
std::stoi(ctElements[12])));
else
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
}
} else {
throw (std::string("Rules i1 < i1' and i1' < j1' and j1' < j1 and i2 < i2' and i2' < j2' and j2' < j2 are not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
// Add internal loop to ctIntLoop
void addIntLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Interloop * >& ctIntLoop,
std::string CTfile, int nLine) {
int i, j, ibis, jbis, l1, l2;
try {
if (int(ctElements.size()) >= 9) { // Name1 \space IDmotif \space i \s i' \s j' \s j \s length1 \s length2 \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[2], ctElements[3], ctElements[4], ctElements[5]},
rnaList_[rna1].get_n_())
and checkLength({ctElements[6], ctElements[7]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[8])) {
i = std::stoi(ctElements[2]);
ibis = std::stoi(ctElements[3]);
jbis = std::stoi(ctElements[4]);
j = std::stoi(ctElements[5]);
l1 = std::stoi(ctElements[6]);
l2 = std::stoi(ctElements[7]);
if (i < ibis and ibis < jbis and jbis < j) {
// there is an internal loop with no information
if(i == 0 and j == 0 and ibis == 0 and jbis == 0 and l1 == 0 and l2 == 0)
ctIntLoop.push_back(new Interloop (int(rna1), rnaList_[rna1].get_seq_(), -1, -1, -1, -1, -1, -1));
else {
if (l1 != 0 and i != 0)
ibis = i+l1+1;
if (l1 != 0 and ibis != 0)
i = ibis-l1-1;
if (l2 != 0 and jbis != 0)
j = jbis+l2+1;
if (l2 != 0 and j != 0)
jbis = j-l2-1;
if (i != 0 and ibis != 0)
l1 = ibis-i-1;
if (jbis != 0 and j != 0)
l2 = j-jbis-1;
// there is an internal loop with all information
if(i != 0 and j != 0 and ibis != 0 and jbis != 0 and l1 != 0 and l2 != 0)
ctIntLoop.push_back(new Interloop (int(rna1), rnaList_[rna1].get_seq_(),
i-1, ibis-1, j-1, jbis-1, l1, l2, std::stoi(ctElements[8])));
// there is an internal loop with length information
else if (l1 != 0 and l2 != 0)
ctIntLoop.push_back(new Interloop (int(rna1), rnaList_[rna1].get_seq_(),
-1, -1, -1, -1, l1, l2, std::stoi(ctElements[8])));
else
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
}
} else {
throw (std::string("Rules i < i' and i' < j' and j' < j are not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
// Add hairpin loop to ctHairLoop
void addHairLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Hairpinloop * >& ctHairLoop,
std::string CTfile, int nLine) {
int i, j, l1;
try {
if (int(ctElements.size()) >= 5) { // Name1 \space IDmotif \space i \s j \s length \s ic
// Check base indexes and confidance index
if (checkIndex({ctElements[2], ctElements[3]}, rnaList_[rna1].get_n_())
and checkLength({ctElements[4]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[5])) {
i = std::stoi(ctElements[2]);
j = std::stoi(ctElements[3]);
l1 = std::stoi(ctElements[4]);
if (i <= j) {
if(i == 0 and j == 0 and l1 == 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), -1, -1, -1, std::stoi(ctElements[5])));
else if (i != 0 and j != 0 and l1 != 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), i-1, j-1, l1, std::stoi(ctElements[5])));
else if (i == 0 and j == 0 and l1 != 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), -1, -1, l1, std::stoi(ctElements[5])));
else if (i == 0 and l1 != 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), j-l1-1, j-1, l1, std::stoi(ctElements[5])));
else if (j == 0 and l1 != 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), i-1, i+l1, l1, std::stoi(ctElements[5])));
else if (l1 == 0)
ctHairLoop.push_back(new Hairpinloop(int(rna1), rnaList_[rna1].get_seq_(), i-1, j-1, j-i-1, std::stoi(ctElements[5])));
else
throw (std::string("Missing information in indexes : either all indexes and length, or all indexes,"
" or all length sould be provided. Please look at the documentation."));
} else {
throw (std::string("Rule i < j is not respected."));
}
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
// Add multijunction loop to ctMultiLoop
void addMultiLoop(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < Multiloop * >& ctMultiLoop,
std::string CTfile, int nLine) {
std::vector < int > indexes;
int ic;
std::vector < std::pair < int, int > > ctMulti;
bool cond = true;
try {
if (ctElements.size()%2 == 1) {
for (size_t i = 2, size = ctElements.size(); i != size and cond; i++) {
if (i != size-1) {
if (checkBasePairIndex({ctElements[i]}, rnaList_[rna1].get_n_())) {
indexes.push_back(std::stoi(ctElements[i]));
} else {
cond = false;
}
} else if (checkIC(ctElements[i])) {
ic = std::stoi(ctElements[i]);
} else {
cond = false;
}
}
if (!cond) {
throw (std::string("The format is not correct."));
}
// Recover base pair
for(int i = 0, size = int(indexes.size())-1; i != size and cond; i++) {
if (indexes[i] < indexes[i+1]) {
ctMulti.push_back(std::make_pair(indexes[i], indexes[i+1]));
} else {
cond = false;
}
}
// Add Multiloop
if (ctMulti.empty())
ctMultiLoop.push_back(new Multiloop(rna1, rnaList_[rna1].get_seq_(), std::vector < std::pair < int, int > > (), ic));
else {
ctMultiLoop.push_back(new Multiloop(rna1, rnaList_[rna1].get_seq_(), ctMulti, ic));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
// Add base pair to ctApp and ctAppTwo
void addBp(int rna1, int rna2, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_,
std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
std::vector< std::tuple < uint, uint, uint > >& ctApp,
std::string CTfile, int nLine) {
try {
if (rna1 != rna2 and int(ctElements.size()) >= 6) { // Name1 \space Name2 \space IDmotif \space i \s j \s ic
// Check base indexes and confidance index
if (checkBasePairIndex({ctElements[3]}, rnaList_[rna1].get_n_())
and checkIndex({ctElements[4]}, rnaList_[rna2].get_n_())
and checkIC(ctElements[5])) {
if(std::stoi(ctElements[4]) == 0)
ctApp.push_back(std::make_tuple(rna1, std::stoi(ctElements[3])-1, std::stoi(ctElements[5])));
else
ctAppTwo.push_back(std::make_tuple(std::make_pair(rna1, std::stoi(ctElements[3])-1),
std::make_pair(rna2, std::stoi(ctElements[4])-1),
std::stoi(ctElements[5])));
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else if ( rna1 == rna2 and int(ctElements.size()) >= 5) { // Name1 \space IDmotif \space i \s j \s ic
// Check base indexes and confidance index
if (checkBasePairIndex({ctElements[2]}, rnaList_[rna1].get_n_())
and checkIndex({ctElements[3]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[4])) {
if(std::stoi(ctElements[3]) == 0)
ctApp.push_back(std::make_tuple(rna1, std::stoi(ctElements[2])-1, std::stoi(ctElements[4])));
else
ctAppTwo.push_back(std::make_tuple(std::make_pair(rna1, std::stoi(ctElements[2])-1),
std::make_pair(rna1, std::stoi(ctElements[3])-1),
std::stoi(ctElements[4])));
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
// Add alone pair to ctSingle
void addSingle(int rna1, const std::vector < std::string > &ctElements,
const std::vector < Rna >& rnaList_, std::vector < std::tuple < uint, uint, uint > >& ctSingle,
std::string CTfile, int nLine) {
try {
if (int(ctElements.size()) >= 5) { // Name1 \space IDmotif \space i \s ic
// Check base indexes and confidance index
if (checkBasePairIndex({ctElements[2]}, rnaList_[rna1].get_n_())
and checkIC(ctElements[3])) {
ctSingle.push_back(std::make_tuple(rna1, std::stoi(ctElements[2])-1, std::stoi(ctElements[3])));
} else {
throw (std::string("Index of a base, the length or the confidence index is not correct. Should be between 0 and length of the RNA."));
}
} else {
throw (std::string("The format of is not correct."));
}
} catch (std::string e) {
throw (std::string("Error in the constraint file " + CTfile + ", line " +
std::to_string(nLine) + ".\n" + e));
}
}
void extract_ct(const std::string CTfile, const std::vector < Rna >& rnaList_,
std::vector< std::tuple < std::pair < uint, uint >, std::pair < uint, uint >, uint > >& ctAppTwo,
std::vector< std::tuple < uint, uint, uint > >& ctApp,
std::vector< std::tuple < uint, uint, uint > >& ctSingle,
std::vector < Interloop * >& ctIntLoop,
std::vector < Hairpinloop * >& ctHairLoop,
std::vector < Helix * >& ctHelix,
std::vector < Multiloop * >& ctMultiLoop,
std::vector < Pseudoknot * >& ctPseudo)
{
struct stat buf;
if( (stat(CTfile.c_str(), &buf) == 0)) {
std::string name1 = "", name2 = "", idMotif = "", line = "";
std::vector< std::string > ctElements;
std::vector< std::string > motifs = {"B", "A", "H", "I", "M", "S", "P"};
std::vector < int > cts;
size_t k, size;
int nLine = 1;
int rna1, rna2; // the RNA index
std::ifstream ifs(CTfile);
while (std::getline(ifs, line)) {
if (line.compare("\n") != 0 and line[0] != '#' and line != "") {
//std::cout << "nLine : " << nLine << std::endl;
ctElements.clear();
boost::split( ctElements, line, boost::is_any_of(" \t"), boost::token_compress_on );
/*std::cout << "line " << nLine << ": ";
for(size_t i = 0, size = ctElements.size(); i != size; i++)
std::cout << ctElements[i] << " ";
std::cout << std::endl;*/
if(int(ctElements.size()) >= 2) { // Name1 \space (Name2) \space IDmotif \space (depending on IDmotif optional)
// Check RNA indexes
name1 = "";
name2 = "";
name1 = ctElements[0];
name2 = ctElements[1];
rna1 = -1;
rna2 = -1;
for (k = 0, size = rnaList_.size(); k != size; k++)
if (name1.compare(rnaList_[k].get_name_()) == 0)
rna1 = k;
for (k = 0, size = rnaList_.size(); k != size; k++)
if (name2.compare(rnaList_[k].get_name_()) == 0)
rna2 = k;
if (rna2 == -1) { // Check idMotif if not rna2
idMotif = "";
for (k = 0, size = motifs.size(); k != size; k++)
if (ctElements[1].compare(motifs[k]) == 0)
idMotif = ctElements[1];
}
if (rna1 != -1 and rna2 != -1) { // Interaction motif: RNA indexes are ok
if(int(ctElements.size()) >= 3) { // Name1 \space (Name2) \space IDmotif \space (depending on IDmotif optional)
// Check idMotif
idMotif = "";
for (k = 0, size = motifs.size(); k != size; k++)
if (ctElements[2].compare(motifs[k]) == 0)
idMotif = ctElements[2];
try {
if (idMotif.compare("B") == 0) {
addBp(rna1, rna2, ctElements, rnaList_,
ctAppTwo, ctApp, CTfile, nLine);
} else if (idMotif.compare("S") == 0) {
addHelix(rna1, rna2, ctElements,
rnaList_, ctHelix,
CTfile, nLine);
} else if (idMotif.compare("P") == 0) {
addPseudo(rna1, rna2, ctElements, rnaList_,
ctPseudo, CTfile, nLine);
} else {
throw (std::string("The motif id " + idMotif + ", line " + std::to_string(nLine) +
" of the constraint file is not correct."));
}
} catch (std::string e) {
throw (e);
}
} else {
throw (std::string("The format of the constraint file " + CTfile + ", line " + std::to_string(nLine) +
" is not correct. Please look at the example inputs."));
}
} else if (rna1 != -1 and idMotif != "") { // Structure motif: RNA index and idMotif is ok
try {
if (idMotif.compare("B") == 0) {
addBp(rna1, rna1, ctElements, rnaList_,
ctAppTwo, ctApp, CTfile, nLine);
} else if (idMotif.compare("A") == 0) {
addSingle(rna1, ctElements, rnaList_,
ctSingle, CTfile, nLine);
} else if (idMotif.compare("H") == 0) {
addHairLoop(rna1, ctElements, rnaList_,
ctHairLoop, CTfile, nLine);
} else if (idMotif.compare("I") == 0) {
addIntLoop(rna1, ctElements, rnaList_,
ctIntLoop, CTfile, nLine);
} else if (idMotif.compare("M") == 0) {
addMultiLoop(rna1, ctElements, rnaList_,
ctMultiLoop, CTfile, nLine);
} else if (idMotif.compare("S") == 0) {
addHelix(rna1, rna1, ctElements,
rnaList_, ctHelix,
CTfile, nLine);
} else if (idMotif.compare("P") == 0) {
addPseudo(rna1, rna1, ctElements, rnaList_,
ctPseudo, CTfile, nLine);
} else {
throw (std::string("The motif id " + idMotif + ", line " + std::to_string(nLine) +
" of the cosntraint file is not correct."));
}
} catch (std::string e) {
throw (e);
}
} else if (rna1 == -1 and rna2 == -1) {
throw (std::string("The RNAs " + name1 + " and " + name2 + " do not exist in the fasta file. Found in constraint 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 constraint file line " +
std::to_string(nLine) + "."));
} else if (rna2 == -1 or idMotif == "") {
throw (std::string("The RNA or motif id " + name2 + " does not exist. Found in constraint file line " +
std::to_string(nLine) + "."));
}
} else {
throw (std::string("The format of the constraint file " + CTfile + ", line " +
std::to_string(nLine) + " is not correct. Please look at the example inputs."));
}
}
nLine++;
}
}
else
{
throw (std::string("The file " + CTfile + " doesn't exist."));
}
#ifdef _DEBUG
std::cout << "fin extract_ct" << std::endl;
#endif
}