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/*
* Pgencounter.cpp
*
* Created on: Aug 19, 2016
* Author: Quentin Marcou
*
* This source code is distributed as part of the IGoR software.
* IGoR (Inference and Generation of Repertoires) is a versatile software to analyze and model immune receptors
* generation, selection, mutation and all other processes.
* Copyright (C) 2017 Quentin Marcou
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
#include "Pgencounter.h"
using namespace std;
Pgen_counter::Pgen_counter(): Pgen_counter("/tmp/" , false) {
}
Pgen_counter::Pgen_counter(std::string path): Pgen_counter(path , true) {
}
Pgen_counter::Pgen_counter(std::string path , bool output_Pgen_estimator_only , bool do_output_sequences): Counter(path) , output_sequences(do_output_sequences) , output_Pgen_estimator(output_Pgen_estimator_only) , sequence_Pgens_map(unordered_map<Int_Str,pair<double,long double>>()) , scenario_resulting_sequence(Int_Str()) , read_likelihood(0) , v_gene(false) , d_gene(false) , j_gene(false) , vd_ins(false) , dj_ins(false) , vj_ins(false){
if(output_Pgen_estimator and output_sequences){
throw invalid_argument("Cannot set both \"output_Pgen_estimator_only\" and \"do_output_sequences\" to true. Pgen estimator is one line per read, otherwise every scenario sequence per read");
}
this->last_iter_only = true;
}
Pgen_counter::~Pgen_counter() {
// TODO Auto-generated destructor stub
}
void Pgen_counter::initialize_counter(const Model_Parms& parms , const Model_marginals& marginals){
if(not fstreams_created){
output_pgen_file_ptr = shared_ptr<ofstream>(new ofstream);
output_pgen_file_ptr->open(path_to_file + "Pgen_counts.csv");
//Create the header
if(output_Pgen_estimator){
(*output_pgen_file_ptr.get())<<"seq_index;Pgen_estimate"<<endl;
}
else{
if(output_sequences){
(*output_pgen_file_ptr.get())<<"seq_index;scen_sequence;Pgen;P_joint_read_seq"<<endl;
}
else{
(*output_pgen_file_ptr.get())<<"seq_index;Pgen;P_seq_given_read"<<endl;
}
}
fstreams_created = true;
}
const unordered_map<tuple<Event_type,Gene_class,Seq_side>, shared_ptr<Rec_Event>>& events_map = parms.get_events_map();
//Initialize booleans for constructed sequences
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(GeneChoice_t,V_gene,Undefined_side))>0){
v_gene=true;
}
else{v_gene=false;}
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(GeneChoice_t,D_gene,Undefined_side))>0){
d_gene=true;
}
else{d_gene=false;}
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(GeneChoice_t,J_gene,Undefined_side))>0){
j_gene=true;
}
else{j_gene=false;}
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(Insertion_t,VJ_genes,Undefined_side))>0){
vj_ins=true;
}
else{vj_ins=false;}
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(Insertion_t,VD_genes,Undefined_side))>0){
vd_ins=true;
}
else{vd_ins=false;}
if(events_map.count(tuple<Event_type,Gene_class,Seq_side>(Insertion_t,DJ_genes,Undefined_side))>0){
dj_ins=true;
}
else{dj_ins=false;}
}
void Pgen_counter::count_scenario(long double scenario_seq_joint_proba , double scenario_probability , const string& original_sequence , Seq_type_str_p_map& constructed_sequences , const Seq_offsets_map& seq_offsets , const unordered_map<tuple<Event_type,Gene_class,Seq_side>, shared_ptr<Rec_Event>>& events_map , Mismatch_vectors_map& mismatches_lists ){
scenario_resulting_sequence.clear();
if(v_gene){
scenario_resulting_sequence += (*constructed_sequences[V_gene_seq]);
}
if(d_gene){
if(vd_ins){
scenario_resulting_sequence+=(*constructed_sequences[VD_ins_seq]);
}
scenario_resulting_sequence+=(*constructed_sequences[D_gene_seq]);
if(dj_ins){
scenario_resulting_sequence+=(*constructed_sequences[DJ_ins_seq]);
}
}
else{
if(vj_ins){
scenario_resulting_sequence+=(*constructed_sequences[VJ_ins_seq]);
}
}
if(j_gene){
scenario_resulting_sequence+=(*constructed_sequences[J_gene_seq]);
}
if (sequence_Pgens_map.count(scenario_resulting_sequence)>0){
pair<double,long double>& Pgen_Pjoint_pair = sequence_Pgens_map[scenario_resulting_sequence];
Pgen_Pjoint_pair.first+=scenario_probability;
Pgen_Pjoint_pair.second+=scenario_seq_joint_proba;
}
else{
pair<double,long double>& Pgen_Pjoint_pair = sequence_Pgens_map[scenario_resulting_sequence];
//make proper initialization
Pgen_Pjoint_pair.first=scenario_probability;
Pgen_Pjoint_pair.second=scenario_seq_joint_proba;
}
read_likelihood+=scenario_seq_joint_proba;
}
void Pgen_counter::dump_sequence_data(int seq_index , int iteration_n ){
double log_P_gen_estimate = 0;
for(unordered_map<Int_Str,pair<double,long double>>::const_iterator iter = sequence_Pgens_map.begin() ; iter != sequence_Pgens_map.end() ; ++iter){
if(output_Pgen_estimator){
log_P_gen_estimate += (*iter).second.second/read_likelihood*log((*iter).second.first);
}
else{
if(output_sequences){
//(*output_pgen_file_ptr)<<seq_index<<";"<<(*iter).first<<";"<<(*iter).second.first<<";"<<(*iter).second.second/read_likelihood<<endl;
}
else{
(*output_pgen_file_ptr.get())<<seq_index<<";"<<(*iter).second.first<<";"<<(*iter).second.second/read_likelihood<<endl;
}
}
}
if(read_likelihood == 0.0){
log_P_gen_estimate = std::nan("");
}
if(output_Pgen_estimator){
(*output_pgen_file_ptr.get())<<seq_index<<";"<<exp(log_P_gen_estimate)<<endl;
}
//Reset counters
read_likelihood = 0.0;
sequence_Pgens_map.clear();
}
void Pgen_counter::add_checked(shared_ptr<Counter> counter){
return;
}
shared_ptr<Counter> Pgen_counter::copy() const{
shared_ptr<Pgen_counter> counter_copy_ptr (new Pgen_counter());
counter_copy_ptr->fstreams_created = this->fstreams_created;
counter_copy_ptr->output_Pgen_estimator = this->output_Pgen_estimator;
counter_copy_ptr->output_sequences = this->output_sequences;
if(this->fstreams_created){
counter_copy_ptr->output_pgen_file_ptr = this->output_pgen_file_ptr;
}
else{
throw runtime_error("Counters should not be copied before stream initalization");
}
return counter_copy_ptr;
}
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