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node_within_host.cu
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#include "node_within_host.cuh"
node_within_host::node_within_host()
{
cout << "Intializing host: ";
}
void node_within_host::setHost(int host_Index, int cave_ID, int host_ID, int profile_ID, int num_Tissues)
{
this->host_Index = host_Index;
this->cave_ID = cave_ID;
this->host_ID = host_ID;
this->profile_ID = profile_ID;
this->num_Tissues = num_Tissues;
cout << this->cave_ID << "_" << host_ID << endl;
}
void node_within_host::setNum_Generation(int num_Generation)
{
this->num_Generation = num_Generation;
}
void node_within_host::setInfectious_Load(int infectious_Load)
{
this->infectious_Load = infectious_Load;
}
void node_within_host::setTerminal_Load(int terminal_Load)
{
this->terminal_Load = terminal_Load;
}
void node_within_host::setSampling_Effect(float sampling_Effect)
{
this->sampling_Effect = sampling_Effect;
}
void node_within_host::setCell_Limit(vector<int> cell_Limit_vec)
{
num_Tissues = cell_Limit_vec.size();
this->cell_Limit = (int *)malloc(sizeof(int) * num_Tissues);
for (size_t i = 0; i < num_Tissues; i++)
{
cell_Limit[i] = cell_Limit_vec[i];
}
}
void node_within_host::print_All()
{
cout << host_Index << "\t"
<< cave_ID << "_" << host_ID << "\t"
<< profile_ID << "\t"
<< num_Generation << "\t"
<< infectious_Load << "\t"
<< terminal_Load << "\t"
<< sampling_Effect;
for (size_t i = 0; i < num_Tissues; i++)
{
cout << "\t" << cell_Limit[i];
}
cout << endl;
}
void node_within_host::begin_Infection(functions_library &functions, string &intermediary_Sequence_location,
int entry_tissues, int *entry_array, int &max_sequences_per_File,
string &output_Node_location,
vector<string> &tissue_Names, string first_Infection)
{
// FIRST NODE OF INFECTION IN THE HOST
string host_Folder = intermediary_Sequence_location + "/" + to_string(host_Index);
functions.config_Folder(host_Folder, to_string(cave_ID) + "_" + to_string(host_ID));
vector<vector<string>> tissue_Sequences;
intialize_Tissues(host_Folder, tissue_Sequences, functions);
string reference_Sequences = intermediary_Sequence_location + "/reference_Sequences";
cout << "\nFirst infection mode: " << first_Infection << endl;
if (first_Infection == "RANDOM")
{
vector<string> files;
for (const auto &entry : filesystem::directory_iterator(reference_Sequences))
{
if (entry.is_regular_file() && entry.path().extension() == ".nfasta")
{
files.push_back(entry.path().string());
}
}
vector<string> Sequences;
vector<string> Sequence_IDs;
cout << endl;
vector<char> seq_Status;
for (int file = 0; file < files.size(); file++)
{
cout << "Reading file: " << files[file] << endl;
fstream nfasta;
nfasta.open(files[file], ios::in);
if (nfasta.is_open())
{
string line;
string sequence = "";
while (getline(nfasta, line))
{
if (line.at(0) != '>')
{
sequence.append(line);
}
else
{
Sequence_IDs.push_back(line);
if (sequence != "")
{
Sequences.push_back(sequence);
sequence = "";
}
}
}
if (sequence != "")
{
Sequences.push_back(sequence);
sequence = "";
}
nfasta.close();
}
else
{
cout << "ERROR UNABLE TO OPEN NFATSA FILE: " << files[file] << endl;
exit(-1);
}
}
random_device rd; // Will be used to obtain a seed for the random number engine
mt19937 gen(rd());
uniform_int_distribution<int> entry_Tissue_select(0, entry_tissues - 1);
cout << endl;
for (int sequence = 0; sequence < Sequences.size(); sequence++)
{
int tissue_Index = entry_array[entry_Tissue_select(gen)];
cout << "Sequence " << sequence + 1 << " infects tissue: " << tissue_Index << endl;
tissue_Sequences[tissue_Index].push_back(Sequences[sequence]);
}
for (int tissue = 0; tissue < entry_tissues; tissue++)
{
if (tissue_Sequences[entry_array[tissue]].size() > 0)
{
current_Viral_load_per_Tissue[entry_array[tissue]] = tissue_Sequences[entry_array[tissue]].size();
functions.config_Folder(host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), to_string(cave_ID) + "_" + to_string(host_ID) + " Tissue " + to_string(entry_array[tissue]) + " Generation 0");
if (!filesystem::exists(output_Node_location + "/" + get_Name()))
{
functions.config_Folder(output_Node_location + "/" + get_Name(), get_Name() + " node");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", "Sequence_ID\tHost\tTissue");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv", "Source\tTarget\tType");
}
vector<string> sequence_Write_Store_All;
int last_seq_Num = 0;
functions.sequence_Write_Configurator(sequence_Write_Store_All, tissue_Sequences[entry_array[tissue]],
max_sequences_per_File, host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), last_seq_Num, seq_Status,
output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", get_Name(), tissue_Names[entry_array[tissue]], current_Generation);
functions.partial_Write_Check(sequence_Write_Store_All,
host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), last_seq_Num, seq_Status,
output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", get_Name(), tissue_Names[entry_array[tissue]], current_Generation);
}
}
}
else
{
cout << "\nInfecting tissues\n";
vector<string> line_Data;
//// Write to sequence profiles file
for (int tissue = 0; tissue < tissue_Names.size(); tissue++)
{
string reference_Sequences_tissue = reference_Sequences + "/" + tissue_Names[tissue];
int last_seq_Num = 0;
if (filesystem::exists(reference_Sequences_tissue) && filesystem::is_directory(reference_Sequences_tissue))
{
cout << "\nTissue: " << tissue_Names[tissue] << endl;
for (const auto &entry : filesystem::directory_iterator(reference_Sequences_tissue))
{
if (entry.is_regular_file() && entry.path().extension() == ".nfasta")
{
string file_Name = entry.path().stem();
functions.split(line_Data, file_Name, '_');
int num_Particles_Tissue = stoi(line_Data[1]) - stoi(line_Data[0]) + 1;
cout << "Sequences migrating: " << num_Particles_Tissue << endl;
current_Viral_load_per_Tissue[tissue] = current_Viral_load_per_Tissue[tissue] + num_Particles_Tissue;
functions.config_Folder(host_Folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation), to_string(cave_ID) + "_" + to_string(host_ID) + " Tissue " + to_string(tissue) + " Generation 0");
if (!filesystem::exists(output_Node_location + "/" + get_Name()))
{
functions.config_Folder(output_Node_location + "/" + get_Name(), get_Name() + " node");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", "Sequence_ID\tHost\tTissue");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv", "Source\tTarget\tType");
}
filesystem::copy_file(entry.path().string(), host_Folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation) + "/" + file_Name + ".nfasta");
fstream sequence_Profile;
sequence_Profile.open(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", ios::app);
for (int sequence_Num = 0; sequence_Num < num_Particles_Tissue; sequence_Num++)
{
sequence_Profile << get_Name() << "_" << tissue_Names[tissue] << "_" << current_Generation << "_" << last_seq_Num << "\t" << get_Name() << "\t" << tissue_Names[tissue] << endl;
last_seq_Num++;
}
sequence_Profile.close();
}
}
}
}
}
set_Infected();
// exit(-1);
// for (int tissue = 0; tissue < num_Tissues; tissue++)
// {
// cout << current_Viral_load_per_Tissue[tissue] << endl;
// }
// exit(-1);
}
string node_within_host::transfer_Infection(functions_library &functions, string &intermediary_Sequence_location, string &source_Target_file_Location,
int &source_Index, int &source_Generation, string &source_Name, int *source_current_Viral_load_per_Tissue,
int num_viruses_to_transfer,
int &entry_tissues, int *entry_array, int exit_Load, int &exit_tissues, int *exit_array,
vector<set<int>> &source_removed_by_Transfer_Indexes,
int &max_sequences_per_File,
vector<vector<pair<int, int>>> &indexed_Source_Folders,
float &decimal_Date,
string &Host_source_target_network_location,
string &output_Node_location,
vector<string> &tissue_Names,
mt19937 &gen)
{
if (exit_Load > 0)
{
cout << "\nNode " << this->cave_ID << "_" << this->host_ID << " is being infected by " << source_Name << endl;
if (num_viruses_to_transfer > exit_Load)
{
num_viruses_to_transfer = exit_Load;
}
if (num_viruses_to_transfer > 0)
{
string host_Folder = intermediary_Sequence_location + "/" + to_string(host_Index);
int year, month, day;
functions.decimal_to_Date(decimal_Date, year, month, day);
string date_String = to_string(year) + "-" + to_string(month) + "-" + to_string(day);
if (current_Generation == -1)
{
functions.config_Folder(host_Folder, to_string(cave_ID) + "_" + to_string(host_ID));
vector<vector<string>> tissue_Sequences;
intialize_Tissues(host_Folder, tissue_Sequences, functions);
}
cout << "Attempting to transfer " << num_viruses_to_transfer << " viral particle(s)\n";
uniform_int_distribution<> distribution_exit_Tissue(0, exit_tissues - 1);
vector<set<int>> unique_indexes_to_Remove_Tissues;
for (int tissue = 0; tissue < exit_tissues; tissue++)
{
set<int> init_Set;
unique_indexes_to_Remove_Tissues.push_back(init_Set);
}
// cout << "Attempting to transfer " << num_viruses_to_transfer << " viral particle(s)\n";
for (int particle = 0; particle < num_viruses_to_transfer; particle++)
{
int exit_tissue_Index = distribution_exit_Tissue(gen);
if (source_current_Viral_load_per_Tissue[exit_array[exit_tissue_Index]] > 0)
{
uniform_int_distribution<> distribution_particle(0, source_current_Viral_load_per_Tissue[exit_array[exit_tissue_Index]] - 1);
unique_indexes_to_Remove_Tissues[exit_tissue_Index].insert(distribution_particle(gen));
}
}
cout << "Viral particle(s) and their exit tissue(s) have been indentifed\n";
// vector<vector<int>> indexes_to_Remove;
vector<vector<string>> seq_to_Write;
vector<vector<string>> source_Seq_Data;
for (int init = 0; init < entry_tissues; init++)
{
vector<string> initialize;
seq_to_Write.push_back(initialize);
source_Seq_Data.push_back(initialize);
}
uniform_int_distribution<> entry_Select(0, entry_tissues - 1);
for (int tissue = 0; tissue < exit_tissues; tissue++)
{
vector<int> init_Tissue(unique_indexes_to_Remove_Tissues[tissue].begin(), unique_indexes_to_Remove_Tissues[tissue].end());
if (init_Tissue.size() > 0)
{
cout << "Exit tissue: " << exit_array[tissue] + 1 << endl;
vector<int> indexes_of_Seq_write;
for (int transfer_Cell = 0; transfer_Cell < init_Tissue.size(); transfer_Cell++)
{
auto it = source_removed_by_Transfer_Indexes[exit_array[tissue]].find(init_Tissue[transfer_Cell]);
if (it == source_removed_by_Transfer_Indexes[exit_array[tissue]].end())
{
// not present
indexes_of_Seq_write.push_back(init_Tissue[transfer_Cell]);
source_removed_by_Transfer_Indexes[exit_array[tissue]].insert(init_Tissue[transfer_Cell]);
}
}
if (indexes_of_Seq_write.size() > 0)
{
int valid_Sequences = 0;
// cout << "Collecting " << indexes_of_Seq_write.size() << " sequence(s)\n";
vector<string> collected_Sequences = functions.find_Sequences_Master(source_Target_file_Location, indexes_of_Seq_write, exit_array[tissue], indexed_Source_Folders[exit_array[tissue]], source_Generation, valid_Sequences);
cout << "Assinging sequence(s) to entry tissue(s)\n";
if (valid_Sequences != 0)
{
if (!filesystem::exists(output_Node_location + "/" + get_Name()))
{
functions.config_Folder(output_Node_location + "/" + get_Name(), get_Name() + " node");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", "Sequence_ID\tHost\tTissue");
functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv", "Source\tTarget\tType");
}
}
for (int check_Seq = 0; check_Seq < collected_Sequences.size(); check_Seq++)
{
if (collected_Sequences[check_Seq] != "")
{
int entry_Tissue_index = entry_Select(gen);
seq_to_Write[entry_Tissue_index].push_back(collected_Sequences[check_Seq]);
// sequence_Profile << host << "_" << tissue << "_" << last_seq_Num << "\t" << host << tissue<<endl;
source_Seq_Data[entry_Tissue_index].push_back(source_Name + "_" + tissue_Names[exit_array[tissue]] + "_" + to_string(source_Generation) + "_" + to_string(indexes_of_Seq_write[check_Seq]));
}
}
}
}
}
vector<char> seq_Status;
cout << "Writing sequence(s) to entry tissue(s)\n";
int infected_Check = 0;
for (int tissue = 0; tissue < entry_tissues; tissue++)
{
if (seq_to_Write[tissue].size() > 0)
{
if (!filesystem::exists(host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation)))
{
functions.config_Folder(host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), to_string(cave_ID) + "_" + to_string(host_ID) + " Tissue " + to_string(entry_array[tissue]) + " Generation 0");
}
vector<string> sequence_Write_Store_All;
vector<int> indexes_Written;
functions.sequence_Write_Configurator_transfer(sequence_Write_Store_All, seq_to_Write[tissue],
max_sequences_per_File, host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), current_Viral_load_per_Tissue[entry_array[tissue]], seq_Status,
output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", get_Name(), tissue_Names[entry_array[tissue]], current_Generation,
indexes_Written);
functions.partial_Write_Check_transfer(sequence_Write_Store_All,
host_Folder + "/" + to_string(entry_array[tissue]) + "/generation_" + to_string(current_Generation), current_Viral_load_per_Tissue[entry_array[tissue]], seq_Status,
output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", get_Name(), tissue_Names[entry_array[tissue]], current_Generation, indexes_Written);
infected_Check = 1;
//(output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv", "Source\tTarget\tType");
fstream source;
fstream target;
source.open(output_Node_location + "/" + source_Name + "/sequence_parent_Progeny_relationships.csv", ios::app);
target.open(output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv", ios::app);
// functions.create_File(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", "Sequence_ID\tHost\tTissue");
fstream target_Profiles;
target_Profiles.open(output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv", ios::app);
fstream source_Profiles;
source_Profiles.open(output_Node_location + "/" + source_Name + "/sequence_Profiles.csv", ios::app);
for (int transfers = 0; transfers < indexes_Written.size(); transfers++)
{
source << source_Seq_Data[tissue][transfers] << "\t" << get_Name() << "_" << tissue_Names[entry_array[tissue]] << "_" << current_Generation << "_" << to_string(indexes_Written[transfers]) << "\tTransmission" << endl;
target << source_Seq_Data[tissue][transfers] << "\t" << get_Name() << "_" << tissue_Names[entry_array[tissue]] << "_" << current_Generation << "_" << to_string(indexes_Written[transfers]) << "\tTransmission" << endl;
target_Profiles << source_Seq_Data[tissue][transfers] << "\t" << source_Name << "\t" << tissue_Names[entry_array[tissue]] << endl;
source_Profiles << get_Name() << "_" << tissue_Names[entry_array[tissue]] << "_" << current_Generation << "_" << to_string(indexes_Written[transfers]) << "\t" << get_Name() << "\t" << tissue_Names[entry_array[tissue]] << endl;
}
source.close();
target.close();
target_Profiles.close();
}
}
if (infected_Check == 1)
{
if (status == "Susceptible")
{
set_Infected();
}
fstream write_source_Target;
write_source_Target.open(Host_source_target_network_location, ios::app);
if (write_source_Target.is_open())
{
cout << "Writing host's source target relationship\n";
write_source_Target << source_Name << "\t" << this->get_Name() << "\t" << to_string(decimal_Date) << "\t" << date_String << endl;
write_source_Target.close();
}
else
{
cout << "ERROR: UNABLE TO OPEN SOURCE TARGET FILE: " << Host_source_target_network_location << "\n";
exit(-1);
}
}
}
}
else
{
cout << source_Name << " has no viral particles in the exit tissues\n";
}
return status;
}
int node_within_host::get_generation_Phase(int generation, int *num_replication_phases, float **tissue_replication_data, int *tissue_param_profile_Stride, int &tissue,
float &variable_1, float &variable_2)
{
cout << "Getting generation phase\n";
int gen_Phase = -1;
int num_Phases = num_replication_phases[(profile_ID * num_Tissues) + tissue];
int num_phases_per_tissue = 0;
int tissue_Check = 0;
for (int param_Index = tissue_param_profile_Stride[profile_ID]; param_Index < tissue_param_profile_Stride[profile_ID + 1]; param_Index++)
{
if (tissue_Check == tissue)
{
float time_Check = 0;
float current_Generation_Ratio = (float)generation / (float)num_Generation;
for (int phases = param_Index; phases < (param_Index + num_Phases); phases++)
{
time_Check = time_Check + tissue_replication_data[phases][0];
if (current_Generation_Ratio < time_Check)
{
variable_1 = tissue_replication_data[phases][2];
variable_2 = tissue_replication_data[phases][3];
gen_Phase = tissue_replication_data[phases][1];
return gen_Phase;
// break;
}
}
// break;
}
num_phases_per_tissue++;
if (num_phases_per_tissue == num_replication_phases[(profile_ID * num_Tissues) + tissue_Check])
{
num_phases_per_tissue = 0;
tissue_Check++;
}
}
return gen_Phase;
}
void node_within_host::run_Generation(functions_library &functions, string &multi_Read, int &max_Cells_at_a_time, int &gpu_Limit, int *CUDA_device_IDs, int &num_Cuda_devices, int &genome_Length,
int &CPU_cores, int &max_sequences_per_File,
string source_sequence_Data_folder, string &output_Node_location,
vector<string> &tissue_Names,
int *num_replication_phases, float **tissue_replication_data, int *tissue_param_profile_Stride,
int terminal_tissues, int *terminal_array,
int **cell_Distribution_Type, vector<pair<float, float>> &viral_distribution_per_Tissue_param,
float *Reference_fitness_survivability_proof_reading,
int *mutation_recombination_proof_Reading_availability,
int *num_effect_Segregating_sites,
float **sequence_Fitness_changes,
float **sequence_Survivability_changes,
float **sequence_Proof_reading_changes,
int &mutation_Hotspots,
float **mutation_hotspot_parameters,
float **A_0_mutation,
float **T_1_mutation,
float **G_2_mutation,
float **C_3_mutation,
int &recombination_Hotspots,
float **recombination_hotspot_parameters,
int *tot_prob_selectivity,
int *recombination_prob_Stride,
int *recombination_select_Stride,
float **recombination_Prob_matrix,
float **recombination_Select_matrix,
float *progeny_distribution_parameters_Array,
string &viral_Migration,
float **viral_Migration_Values,
int *migration_start_Generation,
int &overall_Generations,
string &infected_to_Recovered,
string enable_Folder_management,
string enable_Compression,
mt19937 &gen)
{
cout << "\nSimulating generation " << current_Generation << " of " << num_Generation << " for " << get_Name() << endl
<< endl;
if (current_Generation < num_Generation)
{
cout << "Calculating actual particles in each tissue: \n";
////clear array
int *real_Particle_count_per_Tissue = (int *)malloc(sizeof(int) * num_Tissues);
int sum_Check = 0;
for (int tissue = 0; tissue < num_Tissues; tissue++)
{
real_Particle_count_per_Tissue[tissue] = current_Viral_load_per_Tissue[tissue] - removed_by_Transfer_Indexes[tissue].size() - dead_Particle_count[tissue];
cout << tissue_Names[tissue] << " tissue: " << real_Particle_count_per_Tissue[tissue] << endl;
sum_Check = sum_Check + real_Particle_count_per_Tissue[tissue];
}
if (sum_Check > 0)
{
if (terminal_status(terminal_tissues, terminal_array, source_sequence_Data_folder, enable_Folder_management, enable_Compression) != 1)
{
cout << "\nInitiating simulation\n";
// cout << profile_ID << endl;
vector<vector<pair<int, int>>> indexed_Source_Folders = functions.index_sequence_Folders(source_sequence_Data_folder, num_Tissues, current_Generation, multi_Read);
string sequence_Profiles = output_Node_location + "/" + get_Name() + "/sequence_Profiles.csv";
string sequence_parent_Progeny_relationships = output_Node_location + "/" + get_Name() + "/sequence_parent_Progeny_relationships.csv";
string generational_Summary = output_Node_location + "/" + get_Name() + "/node_generational_Summary.csv";
if (!filesystem::exists(output_Node_location + "/" + get_Name()))
{
functions.config_Folder(output_Node_location + "/" + get_Name(), get_Name() + " node");
}
if (!filesystem::exists(sequence_Profiles))
{
functions.create_File(sequence_Profiles, "Sequence_ID\tHost\tTissue");
}
if (!filesystem::exists(sequence_parent_Progeny_relationships))
{
functions.create_File(sequence_parent_Progeny_relationships, "Source\tTarget\tType");
}
if (!filesystem::exists(generational_Summary))
{
functions.create_File(generational_Summary, "overall_Generation\tnode_Generation\tTissue\tnum_Parents\tnum_Progeny\tdead_Progeny");
}
for (int tissue = 0; tissue < num_Tissues; tissue++)
{
if (real_Particle_count_per_Tissue[tissue] > 0)
{
// real_Particle_count_per_Tissue[tissue] = 123;
cout << "\nSimulating " << real_Particle_count_per_Tissue[tissue] << " particle(s) for " << tissue_Names[tissue] << " tissue\n"
<< endl;
// cout << profile_ID << endl;
// for (int generation = current_Generation; generation < num_Generation; generation++)
// {
// float variable_1, variable_2;
// int gen_Phase = get_generation_Phase(generation, num_replication_phases, tissue_replication_data, tissue_param_profile_Stride, tissue,
// variable_1, variable_2);
// cout << "Gen phase " << generation << ": " << gen_Phase << endl;
// cout << variable_1 << "\t" << variable_2 << endl;
// }
// exit(-1);
cout << "Identifying indexes to remove\n";
set<int> check_to_Remove;
//// Account for dead file
if (dead_Particle_count[tissue] > 0)
{
cout << "\nIdentifying dead viral indexe(s)\n";
// indexes_of_Dead = (int *)malloc(sizeof(int) * dead_Particle_count[tissue]);
fstream dead_File;
dead_File.open(source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation) + "/dead_List.txt");
if (dead_File.is_open())
{
string line;
// int index = 0;
while (getline(dead_File, line))
{
check_to_Remove.insert(stoi(line));
// index++;
}
dead_File.close();
}
else
{
cout << "ERROR: UNABLE TO OPEN DEAD LIST FILE: " << source_sequence_Data_folder << "/" << tissue << "/generation_" << current_Generation << "/dead_List.txt" << endl;
exit(-1);
}
}
if (removed_by_Transfer_Indexes[tissue].size() > 0)
{
cout << "Identifying transfered viral indexe(s)\n";
for (auto it = removed_by_Transfer_Indexes[tissue].begin(); it != removed_by_Transfer_Indexes[tissue].end(); ++it)
{
int value = *it; // Dereference the iterator to get the value
check_to_Remove.insert(value);
}
}
//// clear 2d
// int *parents_in_Tissue = (int *)malloc(sizeof(int) * real_Particle_count_per_Tissue[tissue]);
//= functions.create_INT_2D_arrays(2, real_Particle_count_per_Tissue[tissue]);
int **parents_in_Tissue;
parents_in_Tissue = (int **)malloc(2 * sizeof(int *));
for (int row = 0; row < 2; row++)
{
parents_in_Tissue[row] = (int *)malloc(real_Particle_count_per_Tissue[tissue] * sizeof(int));
}
// test
// check_to_Remove.insert(0);
// check_to_Remove.insert(1);
// check_to_Remove.insert(5);
// check_to_Remove.insert(99);
// cout << profile_ID << endl;
// for (int generation = current_Generation; generation < num_Generation; generation++)
//{
float variable_1, variable_2;
int gen_Phase = get_generation_Phase(current_Generation, num_replication_phases, tissue_replication_data, tissue_param_profile_Stride, tissue,
variable_1, variable_2);
// cout << "Gen phase " << generation << ": " << gen_Phase << endl;
// cout << variable_1 << "\t" << variable_2 << endl;
// cout << "Gen phase " << generation << ": " << gen_Phase << endl;
// cout << variable_1 << "\t" << variable_2 << endl;
vector<int> start_Stop_cells = assign_Cells(functions, parents_in_Tissue, real_Particle_count_per_Tissue[tissue], tissue,
cell_Distribution_Type[profile_ID][tissue], viral_distribution_per_Tissue_param[tissue].first, viral_distribution_per_Tissue_param[tissue].second,
check_to_Remove,
gen_Phase, variable_1, variable_2,
gen);
check_to_Remove.clear();
removed_by_Transfer_Indexes[tissue].clear();
dead_Particle_count[tissue] = 0;
current_Viral_load_per_Tissue[tissue] = 0;
cout << "Total number of cell(s) infected: " << start_Stop_cells.size() - 1 << endl;
// if (start_Stop_cells.size() - 1 > 0)
// {
// for (int i = 0; i < start_Stop_cells.size() - 1; i++)
// {
// // cout << start_Stop_cells[i] << " : \t" << start_Stop_cells[i + 1] << endl;
// for (int particle = start_Stop_cells[i]; particle < start_Stop_cells[i + 1]; particle++)
// {
// // cout << parents_in_Tissue[0][particle] << " :\t" << parents_in_Tissue[1][particle] << endl;
// cout << parents_in_Tissue[1][particle] << "_" << parents_in_Tissue[0][particle] << ", ";
// }
// cout << endl;
// }
// }
// }
// exit(-1);
// vector<int> start_Stop_cells;
if ((start_Stop_cells.size() - 1) > 0)
{
// cout << "check\n";
// for (int i = 0; i < start_Stop_cells.size(); i++)
// {
// cout << start_Stop_cells[i] << endl;
// }
for (int i = 0; i < start_Stop_cells.size() - 1; i++)
{
// cout << start_Stop_cells[i] << " : \t" << start_Stop_cells[i + 1] << endl;
for (int particle = start_Stop_cells[i]; particle < start_Stop_cells[i + 1]; particle++)
{
// cout << parents_in_Tissue[0][particle] << " :\t" << parents_in_Tissue[1][particle] << endl;
cout << parents_in_Tissue[1][particle] << "_" << parents_in_Tissue[0][particle] << ", ";
}
cout << endl;
}
// exit(-1);
vector<pair<int, int>> cells_Rounds_start_stop;
int full_Rounds = (start_Stop_cells.size() - 1) / max_Cells_at_a_time;
int partial_Rounds = (start_Stop_cells.size() - 1) % max_Cells_at_a_time;
for (int full = 0; full < full_Rounds; full++)
{
int start = full * max_Cells_at_a_time;
int stop = start + max_Cells_at_a_time;
cells_Rounds_start_stop.push_back(make_pair(start, stop));
}
if (partial_Rounds != 0)
{
int start = (start_Stop_cells.size() - 1) - partial_Rounds;
cells_Rounds_start_stop.push_back(make_pair(start, (start_Stop_cells.size() - 1)));
}
int sequence_Count = 0;
int index_Last_Written = 0;
// source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation + 1),
string intermediary_Tissue_folder = source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation + 1);
string dead_List = intermediary_Tissue_folder + "/dead_List.txt";
if (!filesystem::exists(intermediary_Tissue_folder))
{
functions.config_Folder(intermediary_Tissue_folder, to_string(current_Generation + 1) + " generation Tissue " + tissue_Names[tissue] + " sequences");
}
if (!filesystem::exists(dead_List))
{
functions.create_File(dead_List);
}
string cells_of_parents_location = output_Node_location + "/" + get_Name() + "/cells_of_Parents.csv";
string cells_of_progeny_location = output_Node_location + "/" + get_Name() + "/cells_of_Progeny.csv";
if (!filesystem::exists(cells_of_parents_location))
{
functions.create_File(cells_of_parents_location, "Sequence_ID\tParent_Cell_ID");
}
if (!filesystem::exists(cells_of_progeny_location))
{
functions.create_File(cells_of_progeny_location, "Sequence_ID\tProgeny_Cell_ID");
}
// exit(-1);
// size_t arraySize = sizeof(parents_in_Tissue) / sizeof(parents_in_Tissue[0]);
for (int cell_Round = 0; cell_Round < cells_Rounds_start_stop.size(); cell_Round++)
{
int num_of_Cells = cells_Rounds_start_stop[cell_Round].second - cells_Rounds_start_stop[cell_Round].first;
cout << "\nProcessing round " << cell_Round + 1 << " of " << cells_Rounds_start_stop.size() << ": " << num_of_Cells << " cell(s)" << endl;
int seqeunces_to_Process = start_Stop_cells[cells_Rounds_start_stop[cell_Round].second] - start_Stop_cells[cells_Rounds_start_stop[cell_Round].first];
cout << "Processing " << seqeunces_to_Process << " sequence(s) in total\n";
simulate_Cell_replication(functions, multi_Read, gpu_Limit, CUDA_device_IDs, num_Cuda_devices, source_sequence_Data_folder, indexed_Source_Folders[tissue],
CPU_cores, max_sequences_per_File,
genome_Length,
tissue, parents_in_Tissue, tissue_Names[tissue],
start_Stop_cells, cells_Rounds_start_stop[cell_Round].first, cells_Rounds_start_stop[cell_Round].second, num_of_Cells,
seqeunces_to_Process,
sequence_Count,
Reference_fitness_survivability_proof_reading,
mutation_recombination_proof_Reading_availability,
num_effect_Segregating_sites,
sequence_Fitness_changes,
sequence_Survivability_changes,
sequence_Proof_reading_changes,
mutation_Hotspots,
mutation_hotspot_parameters,
A_0_mutation,
T_1_mutation,
G_2_mutation,
C_3_mutation,
recombination_Hotspots,
recombination_hotspot_parameters,
tot_prob_selectivity,
recombination_prob_Stride,
recombination_select_Stride,
recombination_Prob_matrix,
recombination_Select_matrix,
progeny_distribution_parameters_Array,
cells_of_parents_location,
dead_List, sequence_Profiles, sequence_parent_Progeny_relationships, cells_of_progeny_location,
index_Last_Written,
gen);
}
// free(parents_in_Tissue);
write_Partial_Sequence_Progeny(functions,
intermediary_Tissue_folder,
dead_List,
index_Last_Written,
tissue);
// cout << "\nCount\n";
// cout << dead_Particle_count[tissue] << endl
// << current_Viral_load_per_Tissue[tissue] << endl;
// // TODO: COMPRESS THE PREVIOUS GENERAIONS (Current generations) SEQUENCES per tissue FOLDER
if (enable_Folder_management == "YES")
{
compress_Folder(source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation), enable_Compression);
}
}
cout << "Clearing parent cell array: ";
functions.clear_Array_int_CPU(parents_in_Tissue, 2);
cout << "cleared" << endl;
}
else
{
removed_by_Transfer_Indexes[tissue].clear();
dead_Particle_count[tissue] = 0;
current_Viral_load_per_Tissue[tissue] = 0;
if (enable_Folder_management == "YES")
{
if (filesystem::exists(source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation)))
{
compress_Folder(source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(current_Generation), enable_Compression);
}
}
}
// cout << "Cell Limit: " << cell_Limit[tissue] << endl;
// cout << "Distribution type: " << cell_Distribution_Type[profile_ID][tissue] << endl;
// cout << viral_distribution_per_Tissue_param[tissue].first << "\t" << viral_distribution_per_Tissue_param[tissue].second << endl;
// // TODO: Write per node generational summary
fstream generational_Summary_File;
generational_Summary_File.open(generational_Summary, ios::app);
if (generational_Summary_File.is_open())
{
// overall_Generation\tnode_Generation\tTissue\tnum_Parents\tnum_Progeny\tdead_Progeny
generational_Summary_File << to_string(overall_Generations)
<< "\t" << to_string(current_Generation)
<< "\t" << tissue_Names[tissue]
<< "\t" << to_string(parents_Prev_generation[tissue])
<< "\t" << to_string(current_Viral_load_per_Tissue[tissue])
<< "\t" << to_string(dead_Particle_count[tissue]) << endl;
generational_Summary_File.close();
}
else
{
cout << "ERROR: UNABLE TO OPEN NODE GENERATIONAL SUMMARY FILE: " << generational_Summary << endl;
exit(-1);
}
}
// particle migration between tissues
current_Generation++;
// for (int tissue = 0; tissue < num_Tissues; tissue++)
// {
// cout << "Tissue: " << tissue << endl;
// cout << "\nCount\n";
// cout << dead_Particle_count[tissue] << endl
// << current_Viral_load_per_Tissue[tissue] << endl;
// }
if (viral_Migration == "YES")
{
// TEST SOME more
particle_Migration_between_Tissues(functions,
viral_Migration_Values,
migration_start_Generation,
source_sequence_Data_folder,
tissue_Names,
sequence_parent_Progeny_relationships, sequence_Profiles,
gen);
}
// exit(-1);
}
}
else
{
if (infected_to_Recovered == "NO")
{
set_Removed();
if (enable_Folder_management == "YES")
{
compress_Folder(source_sequence_Data_folder, enable_Compression);
}
clear_Arrays_end();
}
else
{
set_Susceptible();
}
}
free(real_Particle_count_per_Tissue);
}
else
{
set_Removed();
if (enable_Folder_management == "YES")
{
compress_Folder(source_sequence_Data_folder, enable_Compression);
}
}
// get each tissues generational phase
}
void node_within_host::compress_Folder(string path, string &enable_Compression)
{
if (filesystem::exists(path))
{
cout << "\nCompressing folder: " << path << endl;
string tar_Folder;
string command_Tar;
if (enable_Compression == "YES")
{
tar_Folder = path + ".tar.gz";
command_Tar = "tar -czf " + tar_Folder + " " + path + " && rm -R " + path;
}
else
{
tar_Folder = path + ".tar";
command_Tar = "tar -cf " + tar_Folder + " " + path + " && rm -R " + path;
}
int result = system(command_Tar.c_str());
if (result == 0)
{
cout << "Compression successful" << endl;
}
else
{
cout << "Failed to compress the folder: " << path << endl;
exit(-1);
}
}
else
{
cout << "COMPRESSION ERROR: UNABLE TO FIND THE FOLDER: " << path << endl;
exit(-1);
}
}
void node_within_host::compress_Folder(string path, string enable_Compression, int thread)
{
if (filesystem::exists(path))
{
cout << "\nCompressing folder: " << path << endl;
string tar_Folder;
string command_Tar;
if (enable_Compression == "YES")
{
tar_Folder = path + ".tar.gz";
command_Tar = "tar -czf " + tar_Folder + " " + path + " && rm -R " + path;
}
else
{
tar_Folder = path + ".tar";
command_Tar = "tar -cf " + tar_Folder + " " + path + " && rm -R " + path;
}
int result = system(command_Tar.c_str());
if (result == 0)
{
cout << "Compression successful: " << path << endl;
}
else
{
cout << "Failed to compress the folder: " << path << endl;
exit(-1);
}
}
else
{
cout << "COMPRESSION ERROR: UNABLE TO FIND THE FOLDER: " << path << endl;
exit(-1);
}
}