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Commit 4ac06a66 authored by LUISELLI Juliette's avatar LUISELLI Juliette
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Changing the data we record in eukaryote mode

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src/libaevol/7/Stats_7.cpp
+ 55
− 20
View file @ 4ac06a66
...@@ -99,9 +99,10 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or ...@@ -99,9 +99,10 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or
if (is_indiv_) { if (is_indiv_) {
#ifdef __EUKARYOTE #ifdef __EUKARYOTE
statfile_best_ << "Generation" << "," <<"pop_size"<<"," << "fitness" << "," << "metabolic_error" << "," << statfile_best_ << "Generation" << "," <<"pop_size"<<"," << "fitness" << "," << "metabolic_error" << "," <<
"amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
"nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut_total";
#else #else
statfile_best_ << "Generation" << "," <<"pop_size"<<","<<"nb_clones"<<"," << "fitness" << "," << "metabolic_error" << "," << statfile_best_ << "Generation" << "," <<"pop_size"<<","<<"nb_clones"<<"," << "fitness" << "," << "metabolic_error" << "," <<
#endif
"amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," << "amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
"nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut" "nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut"
<< "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," << << "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," <<
...@@ -113,8 +114,12 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or ...@@ -113,8 +114,12 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or
<< "," << "nb_TF" << "," << "nb_pure_TF" << "," << "nb_TF" << "," << "nb_pure_TF"
#endif #endif
; ;
#endif
if (non_coding) { if (non_coding) {
#ifdef __EUKARYOTE
statfile_best_<<","<<"nb_bp_not_essential_incl_non_func_genes";
#else
statfile_best_<< ","<< "nb_bp_not_incl_cds" << "," << statfile_best_<< ","<< "nb_bp_not_incl_cds" << "," <<
"nb_bp_not_incl_func_cds" << "," << "nb_bp_not_incl_func_cds" << "," <<
"nb_bp_not_incl_non_func_cds" << "," << "nb_bp_not_incl_non_func_cds" << "," <<
...@@ -123,15 +128,18 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or ...@@ -123,15 +128,18 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or
"nb_bp_not_incl_non_coding_rna" << "," << "nb_bp_not_incl_non_coding_rna" << "," <<
"nb_bp_not_essential" << "," << "nb_bp_not_essential" << "," <<
"nb_bp_not_essential_incl_non_func_genes"; "nb_bp_not_essential_incl_non_func_genes";
#endif
} }
statfile_best_<< std::endl; statfile_best_<< std::endl;
statfile_best_.flush(); statfile_best_.flush();
} else { } else {
#ifdef __EUKARYOTE #ifdef __EUKARYOTE
statfile_mean_ << "Generation" << "," <<"pop_size"<<","<< "fitness" << "," << "metabolic_error" << "," << statfile_mean_ << "Generation" << "," <<"pop_size"<<","<< "fitness" << "," << "metabolic_error" << "," <<
"amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
"nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut" << ","
<< "nb_bp_not_essential_incl_non_func_genes"
#else #else
statfile_mean_ << "Generation" << "," <<"pop_size"<<","<<"nb_clones"<< "," << "fitness" << "," << "metabolic_error" << "," << statfile_mean_ << "Generation" << "," <<"pop_size"<<","<<"nb_clones"<< "," << "fitness" << "," << "metabolic_error" << "," <<
#endif
"amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," << "amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
"nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut" "nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut"
<< "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," << << "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," <<
...@@ -142,6 +150,7 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or ...@@ -142,6 +150,7 @@ Stats_7::Stats_7(ExpManager_7* simd_individual, int64_t generation, bool best_or
<< "," << "avg_influence" << "," << "avg_pos_influence" << "," << "avg_neg_influence" << "," << "avg_influence" << "," << "avg_pos_influence" << "," << "avg_neg_influence"
<< "," << "nb_TF" << "," << "nb_pure_TF" << "," << "nb_TF" << "," << "nb_pure_TF"
#endif #endif
#endif
<< std::endl; << std::endl;
statfile_mean_.flush(); statfile_mean_.flush();
} }
...@@ -266,6 +275,10 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) { ...@@ -266,6 +275,10 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) {
nb_mut_ = indiv->annotated_chromosome_[A]->dna_->nb_mut_; nb_mut_ = indiv->annotated_chromosome_[A]->dna_->nb_mut_;
#ifndef __EUKARYOTE
double parent_length = indiv->annotated_chromosome_[A]->dna_->parent_length();
nb_rear_ = indiv->annotated_chromosome_[A]->dna_->nb_rear_; nb_rear_ = indiv->annotated_chromosome_[A]->dna_->nb_rear_;
nb_switch_ = indiv->annotated_chromosome_[A]->dna_->nb_swi_; nb_switch_ = indiv->annotated_chromosome_[A]->dna_->nb_swi_;
nb_indels_ = indiv->annotated_chromosome_[A]->dna_->nb_indels_; nb_indels_ = indiv->annotated_chromosome_[A]->dna_->nb_indels_;
...@@ -273,10 +286,12 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) { ...@@ -273,10 +286,12 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) {
nb_del_ = indiv->annotated_chromosome_[A]->dna_->nb_large_del_; nb_del_ = indiv->annotated_chromosome_[A]->dna_->nb_large_del_;
nb_trans_ = indiv->annotated_chromosome_[A]->dna_->nb_large_trans_; nb_trans_ = indiv->annotated_chromosome_[A]->dna_->nb_large_trans_;
nb_inv_ = indiv->annotated_chromosome_[A]->dna_->nb_large_inv_; nb_inv_ = indiv->annotated_chromosome_[A]->dna_->nb_large_inv_;
dupl_rate_ = nb_dupl_ / parent_length;
del_rate_ = nb_del_ / parent_length;
trans_rate_ = nb_trans_ / parent_length;
inv_rate_ = nb_inv_ / parent_length;
double parent_length = indiv->annotated_chromosome_[A]->dna_->parent_length(); #else
#ifdef __EUKARYOTE
amount_of_dna_ += indiv->annotated_chromosome_[B]->dna_->length(); amount_of_dna_ += indiv->annotated_chromosome_[B]->dna_->length();
nb_coding_rnas_ += indiv->annotated_chromosome_[B]->nb_coding_RNAs; nb_coding_rnas_ += indiv->annotated_chromosome_[B]->nb_coding_RNAs;
...@@ -286,21 +301,8 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) { ...@@ -286,21 +301,8 @@ void Stats_7::compute(Individual_7* indiv, bool non_coding) {
nb_non_functional_genes_ += indiv->annotated_chromosome_[B]->nb_non_func_genes; nb_non_functional_genes_ += indiv->annotated_chromosome_[B]->nb_non_func_genes;
nb_mut_ += indiv->annotated_chromosome_[B]->dna_->nb_mut_; nb_mut_ += indiv->annotated_chromosome_[B]->dna_->nb_mut_;
nb_rear_ += indiv->annotated_chromosome_[B]->dna_->nb_rear_;
nb_switch_ += indiv->annotated_chromosome_[B]->dna_->nb_swi_;
nb_indels_ += indiv->annotated_chromosome_[B]->dna_->nb_indels_;
nb_dupl_ += indiv->annotated_chromosome_[B]->dna_->nb_large_dupl_;
nb_del_ += indiv->annotated_chromosome_[B]->dna_->nb_large_del_;
nb_trans_ += indiv->annotated_chromosome_[B]->dna_->nb_large_trans_;
nb_inv_ += indiv->annotated_chromosome_[B]->dna_->nb_large_inv_;
parent_length += indiv->annotated_chromosome_[B]->dna_->parent_length();
#endif #endif
dupl_rate_ = nb_dupl_ / parent_length;
del_rate_ = nb_del_ / parent_length;
trans_rate_ = nb_trans_ / parent_length;
inv_rate_ = nb_inv_ / parent_length;
#ifdef __REGUL #ifdef __REGUL
int32_t nb_activators = 0; int32_t nb_activators = 0;
...@@ -379,6 +381,8 @@ void Stats_7::compute_average(bool non_coding) { ...@@ -379,6 +381,8 @@ void Stats_7::compute_average(bool non_coding) {
for (int indiv_id = 0; indiv_id < pop_size_; indiv_id++) { for (int indiv_id = 0; indiv_id < pop_size_; indiv_id++) {
// simd_individual_->previous_individuals[indiv_id]->compute_phenotype();
if (non_coding) simd_individual_->previous_individuals[indiv_id]->compute_non_coding(); if (non_coding) simd_individual_->previous_individuals[indiv_id]->compute_non_coding();
fitness_ += simd_individual_->previous_individuals[indiv_id]->fitness_; fitness_ += simd_individual_->previous_individuals[indiv_id]->fitness_;
...@@ -393,6 +397,21 @@ void Stats_7::compute_average(bool non_coding) { ...@@ -393,6 +397,21 @@ void Stats_7::compute_average(bool non_coding) {
nb_non_functional_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->nb_non_func_genes; nb_non_functional_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->nb_non_func_genes;
nb_mut_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_mut_; nb_mut_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_mut_;
#ifdef __EUKARYOTE
nb_bases_non_essential_including_nf_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->nb_bases_non_essential_including_nf_genes_;
amount_of_dna_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->dna_->length();
nb_coding_rnas_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->nb_coding_RNAs;
nb_non_coding_rnas_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->nb_non_coding_RNAs;
nb_functional_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->nb_func_genes;
nb_non_functional_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->nb_non_func_genes;
nb_mut_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->dna_->nb_mut_;
nb_bases_non_essential_including_nf_genes_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[B]->nb_bases_non_essential_including_nf_genes_;
#else
nb_rear_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_rear_; nb_rear_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_rear_;
nb_switch_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_swi_; nb_switch_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_swi_;
nb_indels_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_indels_; nb_indels_ += simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->nb_indels_;
...@@ -406,7 +425,7 @@ void Stats_7::compute_average(bool non_coding) { ...@@ -406,7 +425,7 @@ void Stats_7::compute_average(bool non_coding) {
trans_rate_ += trans_rate_ +=
nb_trans_ / simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->parent_length(); nb_trans_ / simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->parent_length();
inv_rate_ += nb_inv_ / simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->parent_length(); inv_rate_ += nb_inv_ / simd_individual_->previous_individuals[indiv_id]->annotated_chromosome_[A]->dna_->parent_length();
#endif
} }
fitness_ /= pop_size_; fitness_ /= pop_size_;
...@@ -419,6 +438,8 @@ void Stats_7::compute_average(bool non_coding) { ...@@ -419,6 +438,8 @@ void Stats_7::compute_average(bool non_coding) {
nb_functional_genes_ /= pop_size_; nb_functional_genes_ /= pop_size_;
nb_non_functional_genes_ /= pop_size_; nb_non_functional_genes_ /= pop_size_;
nb_bases_non_essential_including_nf_genes_ /= pop_size_;
#ifndef __EUKARYOTE
nb_mut_ /= pop_size_; nb_mut_ /= pop_size_;
nb_rear_ /= pop_size_; nb_rear_ /= pop_size_;
nb_switch_ /= pop_size_; nb_switch_ /= pop_size_;
...@@ -432,8 +453,10 @@ void Stats_7::compute_average(bool non_coding) { ...@@ -432,8 +453,10 @@ void Stats_7::compute_average(bool non_coding) {
del_rate_ /= pop_size_; del_rate_ /= pop_size_;
trans_rate_ /= pop_size_; trans_rate_ /= pop_size_;
inv_rate_ /= pop_size_; inv_rate_ /= pop_size_;
#endif
is_computed_ = true; is_computed_ = true;
is_indiv_ = false;
} }
void Stats_7::write_best(bool non_coding) { void Stats_7::write_best(bool non_coding) {
...@@ -462,6 +485,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) { ...@@ -462,6 +485,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) {
statfile_best_<<","<<nb_functional_genes_; statfile_best_<<","<<nb_functional_genes_;
statfile_best_<<","<<nb_non_functional_genes_; statfile_best_<<","<<nb_non_functional_genes_;
statfile_best_<<","<<nb_mut_; statfile_best_<<","<<nb_mut_;
#ifndef __EUKARYOTE
statfile_best_<<","<<nb_switch_; statfile_best_<<","<<nb_switch_;
statfile_best_<<","<<nb_indels_; statfile_best_<<","<<nb_indels_;
statfile_best_<<","<<nb_rear_; statfile_best_<<","<<nb_rear_;
...@@ -473,6 +497,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) { ...@@ -473,6 +497,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) {
statfile_best_<<","<<del_rate_; statfile_best_<<","<<del_rate_;
statfile_best_<<","<<trans_rate_; statfile_best_<<","<<trans_rate_;
statfile_best_<<","<<inv_rate_; statfile_best_<<","<<inv_rate_;
#endif
#ifdef __REGUL #ifdef __REGUL
statfile_best_<< "," << nb_influences_; statfile_best_<< "," << nb_influences_;
statfile_best_<< "," << nb_enhancing_influences_; statfile_best_<< "," << nb_enhancing_influences_;
...@@ -484,6 +509,11 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) { ...@@ -484,6 +509,11 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) {
statfile_best_<< "," << nb_pure_TF_; statfile_best_<< "," << nb_pure_TF_;
#endif #endif
if (non_coding) { if (non_coding) {
#ifdef __EUKARYOTE
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_non_essential_including_nf_genes_ +
indiv->annotated_chromosome_[B]->nb_bases_non_essential_including_nf_genes_;
#else
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_CDS_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_CDS_;
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_functional_CDS_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_functional_CDS_;
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_non_functional_CDS_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_non_functional_CDS_;
...@@ -492,6 +522,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) { ...@@ -492,6 +522,7 @@ void Stats_7::write(Individual_7* indiv,bool non_coding) {
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_non_coding_RNA_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_in_0_non_coding_RNA_;
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_non_essential_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_non_essential_;
statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_non_essential_including_nf_genes_; statfile_best_<< "," << indiv->annotated_chromosome_[A]->nb_bases_non_essential_including_nf_genes_;
#endif
} }
statfile_best_<<std::endl; statfile_best_<<std::endl;
statfile_best_.flush(); statfile_best_.flush();
...@@ -506,15 +537,19 @@ void Stats_7::write_average() { ...@@ -506,15 +537,19 @@ void Stats_7::write_average() {
// Write average stats // Write average stats
#ifdef __EUKARYOTE #ifdef __EUKARYOTE
statfile_mean_<<generation_<<","<<pop_size_<<","<<fitness_<<","<<metabolic_error_<<","<< statfile_mean_<<generation_<<","<<pop_size_<<","<<fitness_<<","<<metabolic_error_<<","<<
amount_of_dna_ << "," << nb_coding_rnas_ << "," << nb_non_coding_rnas_ << "," <<
nb_functional_genes_ << "," << nb_non_functional_genes_ << ","
<< nb_mut_ << "," <<
nb_bases_non_essential_including_nf_genes_ << std::endl;
#else #else
statfile_mean_<<generation_<<","<<pop_size_<<","<<nb_clones_<<","<<fitness_<<","<<metabolic_error_<<","<< statfile_mean_<<generation_<<","<<pop_size_<<","<<nb_clones_<<","<<fitness_<<","<<metabolic_error_<<","<<
#endif
amount_of_dna_<<","<<nb_coding_rnas_<<","<<nb_non_coding_rnas_<<","<< amount_of_dna_<<","<<nb_coding_rnas_<<","<<nb_non_coding_rnas_<<","<<
nb_functional_genes_<<","<<nb_non_functional_genes_<<","<<nb_mut_ nb_functional_genes_<<","<<nb_non_functional_genes_<<","<<nb_mut_
<<","<<nb_switch_<<","<<nb_indels_<<","<<nb_rear_<<","<<nb_dupl_<<","<< <<","<<nb_switch_<<","<<nb_indels_<<","<<nb_rear_<<","<<nb_dupl_<<","<<
nb_del_<<","<<nb_trans_<<","<<nb_inv_<<","<<dupl_rate_<<","<<del_rate_ nb_del_<<","<<nb_trans_<<","<<nb_inv_<<","<<dupl_rate_<<","<<del_rate_
<<","<<trans_rate_<<","<<inv_rate_ <<","<<trans_rate_<<","<<inv_rate_
<<std::endl; <<std::endl;
#endif
statfile_mean_.flush(); statfile_mean_.flush();
} }
} }
......
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