- An RNA sequence (tested with sequences ~100 bases)
- An RNA sequence (with 16 GB of RAM you can go up to ~230 bases)
THEN
-**Pattern-matching step** : Find all possible occurrences of known RNAmodules in the query sequence, by finding subsequences of the querythat score well with the probabilistic models of the modules (like JAR3D, or BayesPairing)
staticuintobj_to_solve_;// What objective do you prefer to solve in mono-objective portions of the algorithm ?
staticdoubleprecision_;// decimals to keep in objective values, to avoid numerical issues. otherwise, solution with objective 5.0000000009 dominates solution with 5.0 =(
staticboolallow_pk_;// Wether we forbid pseudoknots (false) or allow them (true)
staticuintmax_sol_nbr_;// Number of solutions to accept in the Pareto set before we give up the computation
@@ -73,14 +73,15 @@ int main(int argc, char* argv[])
("version","Print the program version")
("seq,s",po::value<string>(&inputName)->required(),"Fasta file containing the RNA sequence")
("descfolder,d",po::value<string>(&motifs_path_name),"A folder containing modules in .desc format, as produced by Djelloul & Denise's catalog program")
("jar3dcsv",po::value<string>(&motifs_path_name),"A file containing the output of JAR3D's search for motifs in the sequence, as produced by test_on_RNAstrand.py")
("bayespaircsv",po::value<string>(&motifs_path_name),"A file containing the output of BayesPairing's search for motifs in the sequence, as produced by test_on_RNAstrand.py")
("jar3dcsv,j",po::value<string>(&motifs_path_name),"A file containing the output of JAR3D's search for motifs in the sequence, as produced by test_on_RNAstrand.py")
("bayespaircsv,b",po::value<string>(&motifs_path_name),"A file containing the output of BayesPairing's search for motifs in the sequence, as produced by test_on_RNAstrand.py")
("first-objective,c",po::value<unsignedint>(&MOIP::obj_to_solve_)->default_value(1),"Objective to solve in the mono-objective portions of the algorithm")
("output,o",po::value<string>(&outputName),"A file to summarize the computation results")
("theta,t",po::value<float>(&theta_p_threshold)->default_value(0.001),"Pairing probability threshold to consider or not the possibility of pairing")
("type,f",po::value<char>(&obj_function_nbr)->default_value('A'),"What objective function to use to include motifs: square of motif size in nucleotides like "
"RNA-MoIP (A), motif size + number of components (B), site score (C), motif size + site score + number of components (D)")
("function,f",po::value<char>(&obj_function_nbr)->default_value('B'),"What objective function to use to include motifs: square of motif size in nucleotides like "
"RNA-MoIP (A), light motif size + high number of components (B), site score (C), light motif size + site score + high number of components (D)")
("disable-pseudoknots,n","Add constraints forbidding the formation of pseudoknots")
("limit,l",po::value<unsignedint>(&MOIP::max_sol_nbr_)->default_value(500),"Intermediate number of solutions in the Pareto set above which we give up the calculation.")
("verbose,v","Print what is happening to stdout");