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removed some comments and help section fixed
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@josura
josura committed Aug 23, 2023
1 parent 106da43 commit 35a40ba
Showing 1 changed file with 6 additions and 16 deletions.
22 changes: 6 additions & 16 deletions src/main.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,6 @@
#include "CustomScalingFunctions.h"


void printHelp(){
//TODO fix this help
std::cout << "usage: ./c2c-sepia --fUniqueGraph <graph>.tsv --fInitialPerturbationPerType <initialPerturbationPerType>.tsv [<subtypes>.txt] --typeInteractionFolder <TypeInteractionFolder>(containing .tsv files)]\nFILE STRUCTURE SCHEMA:\ngraph.tsv\nstart\tend\tweight\n<gene1>\t<gene2>\t <0.something>\n...\n\n\ninitialPerturbationPerType.tsv\n\ttype1\ttype2\t...\ttypeN\ngene1\t<lfc_type1:gene1>\t<lfc_type2:gene1>\t...\t<lfc_typeN:gene1>\ngene1\t<lfc_type1:gene2>\t<lfc_type2:gene2>\t...\t<lfc_typeN:gene2>\n...\n\n\ntypesInteraction.tsv\nstartType:geneLigand\tendType:geneReceptor\tweight\n<type1:geneLigand>\t<type2:genereceptor>\t <0.something>\n...\n\n\nsubtypes.txt\ntype1\ntype3\n..."<<std::endl;
std::cout << "LEGEND:\n <> := placeholder for the name of the file\n[] := optional\n{} := at least one"<<std::endl;
}

int main(int argc, char** argv ) {
//program options
bool ensembleGeneNames=false;
Expand All @@ -32,7 +26,6 @@ int main(int argc, char** argv ) {
bool conservateInitialNorm=false;
namespace po = boost::program_options;
po::options_description desc("Allowed options");
//TODO implement subtypes
desc.add_options()
("help", "() print help section")//<initialPerturbationPerType>.tsv [<subtypes>.txt] [<typesInteraction>.tsv]\nFILE STRUCTURE SCHEMA:\ngraph.tsv\nstart end weight\n<gene1> <gene2> <0.something>\n...\n\n\ninitialPerturbationPerType.tsv\n type1 type2 ... typeN\ngene1 <lfc_type1:gene1> <lfc_type2:gene1> ... <lfc_typeN:gene1>\ngene1 <lfc_type1:gene2> <lfc_type2:gene2> ... <lfc_typeN:gene2>\n...\n\n\ntypesInteraction.tsv\nstartType:geneLigand endType:geneReceptor weight\n<type1:geneLigand> <type2:genereceptor> <0.something>\n...\n\n\nsubtypes.txt\ntype1\ntype3\n...")
("fUniqueGraph", po::value<std::string>(), "(string) graph filename, for an example graph see in resources. NOTE: if this option is chosen, graphsFilesFolder cannot be used")
Expand All @@ -48,7 +41,7 @@ int main(int argc, char** argv ) {
("timestep",po::value<double>(),"timestep to use for the iteration, the final time is iterationIntracell*iterationIntercell*timestep")
("dissipationModel",po::value<std::string>(),"(string) the dissipation model for the computation, available models are: 'none (default)','power','random','periodic','scaled' and 'custom'")
("dissipationModelParameters",po::value<std::vector<double>>()->multitoken(),"(string) the parameters for the dissipation model, for the power dissipation indicate the base, for the random dissipation indicate the min and max value, for the periodic dissipation indicate the period")
("graphsFilesFolder",po::value<std::string>(),"(string) graphs (pathways or other types of graphs) file folder TODO implement different graphs loading")
("graphsFilesFolder",po::value<std::string>(),"(string) graphs (pathways or other types of graphs) file folder")
("conservationModel",po::value<std::string>(),"(string) the conservation model used for the computation, available models are: 'none (default)','scaled','random' and 'custom' ")
("conservationModelParameters", po::value<std::vector<double>>()->multitoken(),"(vector<double>) the parameters for the dissipation model, for the scaled parameter the constant used to scale the conservation final results, in the case of random the upper and lower limit (between 0 and 1)")
("saturation",po::bool_switch(&saturation),"use saturation of values, default to 1, if another value is needed, use the saturationTerm")
Expand All @@ -69,7 +62,6 @@ int main(int argc, char** argv ) {
double timestep = 1;

if (vm.count("help")) {
//printHelp();
std::cout << desc << std::endl;
return 1;
}
Expand Down Expand Up @@ -460,7 +452,6 @@ int main(int argc, char** argv ) {
std::vector<std::string> initialNames = std::get<0>(initialValues);
inputInitials = std::get<2>(initialValues);
std::vector<std::string> typesFromValues = std::get<1>(initialValues);
//TODO understand if types from values should be the same as the types from the graphs since values could be specified for a subset of the types
//this condition should take into account the intersection of the types and the subtypes
if(typesFromValues.size() == 0){
std::cerr << "[ERROR] types from the initial values folder are 0, control if the types are the same to the one specified in the matrix, in the graphs folder and in the subtypes: aborting"<<std::endl;
Expand Down Expand Up @@ -493,7 +484,7 @@ int main(int argc, char** argv ) {
if(indexMapGraphTypesToValuesTypes[i] == -1){
std::cout << "[LOG] type "<<types[i]<<" not found in the initial perturbation files, using zero vector as input"<<std::endl;
std::vector<double> input = std::vector<double>(graphsNodes[i].size(),0);
Computation* tmpCompPointer = new Computation(types[i],input,graphs[i],graphsNodes[i]); //TODO order the genes directly or use the names and set them one by one
Computation* tmpCompPointer = new Computation(types[i],input,graphs[i],graphsNodes[i]);
tmpCompPointer->setDissipationModel(dissipationModel);
tmpCompPointer->setConservationModel(conservationModel);
typeComputations[indexComputation] = tmpCompPointer;
Expand All @@ -502,7 +493,7 @@ int main(int argc, char** argv ) {
} else {
int index = indexMapGraphTypesToValuesTypes[i];
std::vector<double> input = inputInitials[index];
Computation* tmpCompPointer = new Computation(types[i],input,graphs[i],graphsNodes[i]); //TODO order the genes directly or use the names and set them one by one
Computation* tmpCompPointer = new Computation(types[i],input,graphs[i],graphsNodes[i]);
tmpCompPointer->setDissipationModel(dissipationModel);
tmpCompPointer->setConservationModel(conservationModel);
typeComputations[indexComputation] = tmpCompPointer;
Expand All @@ -526,7 +517,6 @@ int main(int argc, char** argv ) {
} else {
typeInteractionsEdges = cellInteractionFileToEdgesListAndNodesByName(*typeInteractionFilename, subtypes, ensembleGeneNames);
}
//TODO insert edges to the correspondent type graph
#pragma omp parallel for
for (uint i = 0; i < types.size();i++) {
if(typeInteractionsEdges.contains(types[i]) && typesIndexes[i] != -1){
Expand Down Expand Up @@ -559,16 +549,16 @@ int main(int argc, char** argv ) {

if (saturation) {
if(vm.count("saturationTerm") == 0){
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2((iterationIntertype*intratypeIterations + iterationIntratype)*timestep, saturation = true); // TODO check if iteration intratype should be multiplied by iteration intertype
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2((iterationIntertype*intratypeIterations + iterationIntratype)*timestep, saturation = true);
} else if (vm.count("saturationTerm") >= 1) {
//TODO create saturation vector
double saturationTerm = vm["saturationTerm"].as<double>();
//TODO TEST
std::vector<double> saturationVector = std::vector<double>(graphsNodes[invertedTypesIndexes[i]].size(),saturationTerm);
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2((iterationIntertype*intratypeIterations + iterationIntratype)*timestep, saturation = true, saturationVector); // TODO check if iteration intratype should be multiplied by iteration intertype
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2((iterationIntertype*intratypeIterations + iterationIntratype)*timestep, saturation = true, saturationVector);
}
} else{
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2(iterationIntertype*intratypeIterations + iterationIntratype, saturation = false); // TODO check if iteration intratype should be multiplied by iteration intertype
std::vector<double> outputValues = typeComputations[i]->computeAugmentedPerturbationEnhanced2(iterationIntertype*intratypeIterations + iterationIntratype, saturation = false);
}
}
//save output values
Expand Down

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