Louis BECQUEY / biorseo

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Louis BECQUEY
b07a46fc 1 parent 494f437b

Working multithreaded loading of .desc files

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Showing 2 changed files with 41 additions and 23 deletions
#include "Motif.h"
#include "Pool.h"
#include <boost/algorithm/string.hpp>
#include <boost/filesystem.hpp>
#include <iostream>
#include <regex>
#include <sstream>
......@@ -34,9 +33,10 @@ Motif::Motif(const vector<Component>& v, string PDB) : comp(v), PDBID(PDB)
}
void Motif::build_from_desc(args_of_parallel_func arg_struct)
// void Motif::build_from_desc(path descfile, string rna, vector<Motif>& final_results)
{
string descfile = arg_struct.descfile;
string rna = arg_struct.rna;
path descfile = arg_struct.descfile;
string& rna = arg_struct.rna;
vector<Motif>& final_results = arg_struct.final_results;
mutex& posInsertionSites_access = arg_struct.posInsertionSites_mutex;
......@@ -50,7 +50,7 @@ void Motif::build_from_desc(args_of_parallel_func arg_struct)
char c = 'a';
char* prev = &c;
motif = std::ifstream(descfile);
motif = std::ifstream(descfile.string());
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) {
......@@ -102,8 +102,10 @@ void Motif::build_from_desc(args_of_parallel_func arg_struct)
for (vector<string>::iterator b = bases.begin() + 1; b < bases.end() - 1; b++) {
int pos = stoi(b->substr(0, b->find('_')));
char nt = b->substr(b->find('_') + 1, 1).back();
if (actual_comp == comp_of_size_1[0]) // we are on the first component of size 1
if (comp_of_size_1.size() and actual_comp == comp_of_size_1[0]) // we are on the first component of size 1
{
b--;
nt = b->substr(b->find('_') + 1, 1).back();
string seq1 = "";
seq1 += nt;
seq1 += "..";
......@@ -123,12 +125,20 @@ void Motif::build_from_desc(args_of_parallel_func arg_struct)
seq = "";
actual_comp++;
comp_of_size_1.erase(comp_of_size_1.begin()); // the first element has been processed, remove it
} else if (actual_comp == comp_of_size_2[0]) { // we are on the first component of size 2
last = pos;
} else if (comp_of_size_2.size() and actual_comp == comp_of_size_2[0]) { // we are on the first component of size 2
b--;
nt = b->substr(b->find('_') + 1, 1).back();
b++; // skip the next nucleotide
char next = b->substr(b->find('_') + 1, 1).back();
last = stoi(b->substr(0, b->find('_')));
string seq1 = "";
seq1 += nt;
seq1 += next;
seq1 += ".";
string seq2 = ".";
seq2 += nt;
seq2 += next;
uint end = motif_variants.size(); // before to add the new one
for (uint u = 0; u < end; ++u) {
motif_variants.push_back(motif_variants[u]); // copy 1 for seq2
......@@ -136,13 +146,12 @@ void Motif::build_from_desc(args_of_parallel_func arg_struct)
motif_variants[u].push_back(seq1);
}
seq = "";
b++; // skip the next nucleotide
actual_comp++;
comp_of_size_2.erase(comp_of_size_1.begin()); // the first element has been processed, remove it
comp_of_size_2.erase(comp_of_size_2.begin()); // the first element has been processed, remove it
} else { // we are on a longer component
if (pos - last > 5) { // finish this component and start a new one
actual_comp++;
for (auto c_s : motif_variants) c_s.push_back(seq);
for (vector<string>& c_s : motif_variants) c_s.push_back(seq);
seq = "";
} else if (pos - last == 2) {
seq += '.';
......@@ -154,10 +163,11 @@ void Motif::build_from_desc(args_of_parallel_func arg_struct)
seq += "....";
}
seq += nt;
last = pos;
}
last = pos;
}
for (auto c_s : motif_variants) c_s.push_back(seq); // pushing the last one after iterating over the bases
for (auto c_s : motif_variants)
if (seq.length()) c_s.push_back(seq); // pushing the last one after iterating over the bases
// We need to search for the different positions where to insert the first component
for (auto c_s : motif_variants) {
......@@ -318,13 +328,14 @@ char Motif::is_valid_DESC(const string& descfile)
vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbose)
{
vector<Motif> posInsertionSites;
mutex posInsertionSites_access;
Pool pool;
int errors = 0;
int accepted = 0;
int inserted = 0;
int num_threads = thread::hardware_concurrency();
vector<Motif> posInsertionSites;
mutex posInsertionSites_access;
Pool pool;
int errors = 0;
int accepted = 0;
int inserted = 0;
// int num_threads = thread::hardware_concurrency();
int num_threads = 4;
vector<thread> thread_pool;
if (!exists(path)) {
......@@ -354,9 +365,10 @@ vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbo
}
accepted++;
if (is_desc_insertible(it.path().string(), rna, verbose)) {
args_of_parallel_func args(it.path().string(), rna, posInsertionSites, posInsertionSites_access);
args_of_parallel_func args(it.path(), rna, posInsertionSites, posInsertionSites_access);
inserted++;
pool.push(bind(Motif::build_from_desc, args));
// Motif::build_from_desc(it.path(), rna, posInsertionSites);
}
}
pool.done();
......@@ -424,7 +436,7 @@ bool is_desc_insertible(const string& descfile, const string& rna, bool verbose)
regex e(seq);
if (regex_search(rna, m, e)) {
if (verbose)
cout << "\t>Motif " << boost::filesystem::path(descfile).stem() << " \t" << seq << "\tcan be inserted ";
cout << "\t>Motif " << boost::filesystem::path(descfile).stem() << " \t" << seq << "\tcan be inserted " << endl;
return true;
} else {
// if (verbose) cout << "Ignoring motif " << descfile.substr(0, descfile.find(".desc")) << " \t" << seq << endl;
......
#ifndef MOTIF_H_
#define MOTIF_H_
#include <boost/filesystem.hpp>
#include <mutex>
#include <string>
#include <vector>
using boost::filesystem::path;
using std::pair;
using std::string;
using std::vector;
......@@ -12,11 +14,14 @@ using std::vector;
class Motif; // forward declaration
typedef struct args_ {
const string& descfile;
path descfile;
string rna;
vector<Motif>& final_results;
std::mutex& posInsertionSites_mutex;
args_(const string& descfile_, string rna_, vector<Motif>& vector_, std::mutex& mutex_) : descfile(descfile_), rna(rna_), final_results(vector_), posInsertionSites_mutex(mutex_){}
args_(path descfile_, string rna_, vector<Motif>& vector_, std::mutex& mutex_)
: descfile(descfile_), rna(rna_), final_results(vector_), posInsertionSites_mutex(mutex_)
{
}
} args_of_parallel_func;
typedef struct Comp_ {
......@@ -37,7 +42,8 @@ class Motif
Motif();
Motif(const vector<Component>& v, string PDB);
void load_from_csv(string csv_line);
static void build_from_desc(args_of_parallel_func arg_struct);
// static void build_from_desc(path descfile, string rna, vector<Motif>& final_results);
static void build_from_desc(args_of_parallel_func args);
static char is_valid_DESC(const string& descfile);
string pos_string(void) const;
string get_origin(void) const;
......