int main() { Config *config=NULL; FileManager fm; FileSet fs; AdvancedScoreModel model; EdgeModel edge_model; PeptideRankScorer drs; rand_seed(112233); // train_all(); model.read_model("CID_IT_TRYP"); config = model.get_config(); config->apply_selected_PTMs("C+57:M+16:Q-17"); // fm.init_from_file(config,"C:\\Work\\msms5\\DnvScore\\all_ds\\HEK_98_3_unique_30.mgf"); fs.select_files_in_mz_range(fm,300,2000,3); fs.randomly_reduce_ssfs(100); vector<int> cc(4,0); cc[3]=100; fs.create_mgf_file(fm,config,"HEK_4_30e.mgf",cc); exit(0); // model.get_config()->apply_selected_PTMs("C+57:M+16:Q-17"); PMCSQS_Scorer *pmcsqs = (PMCSQS_Scorer *)model.get_pmcsqs_ptr(); fm.init_from_list_file(config,"C:\\Work\\msms5\\PepNovoHQ\\train3.txt"); pmcsqs->benchmark_pm_selection(config,fm,0.3); exit(0); /* benchmark_shew(model,"C:\\Work\\msms5\\PepNovoHQ\\Shew_test_10.mgf"); exit(0); drs.set_model_type(0); drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DBSCORE\\DBSCORE_rank_model.txt"); drs.give_de_novo_and_peak_match_examples("C:\\Work\\msms5\\DnvScore\\all_db_hits", "C:\\Work\\msms5\\DnvScore\\seq_freqs\\sequences", "C:\\Work\\msms5\\DnvScore\\dnv_full_parts", "C:\\Work\\msms5\\DnvScore\\dicty2_all.txt", 2,2); exit(0); drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DBSCORE\\DBSCORE_rank_model.txt"); drs.rescore_inspect_results("C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08.mzXML", "C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08.txt", "C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08_new.txt"); exit(0); // test_denovo_integrity(model,"C:\\Work\\msms5\\DnvScore\\all_ds\\Dicty_98_2_unique_8.mgf", 20000, 8); // benchmark_ranking_on_denovo("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVSCORE5\\DNVSCORE5_rank_model.txt", // "C:\\Work\\msms5\\DnvScore\\test\\DNVSCORE4_test_10.mgf",400,10); // // benchmark_ranking_on_full_denovo("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVFULL\\DNVFULL_rank_model.txt", // "C:\\Work\\msms5\\DnvScore\\test\\FULL_test_10.mgf",1000); // exit(0); fm.init_from_list_file(config,//"C:\\Work\\msms5\\DnvScore\\short2_train_mgf_list.txt"); "C:\\Work\\msms5\\DnvScore\\comp2_train_mgf_list.txt"); // "C:\\Work\\msms5\\NewScore\\lists\\Shew_98_3_unique_mgf_list.txt"); fs.select_files(fm,0,2500,-1,-1,2); find_special_PTM_frags_using_offset_counts("S",fm,fs.get_ssf_pointers(),&model,2); exit(0); drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVSC_RANK\\LTQ_DNVRANK_model.txt"); drs.test_model("C:\\Work\\msms5\\DnvScore\\test_sets\\LTQ_DNVRANK_test_10.mgf",2000); drs.train_denovo_partition_model("C:\\Work\\msms5\\DnvScore\\all_db_hits", "C:\\Work\\msms5\\DnvScore\\seq_freqs\\sequences", "C:\\Work\\msms5\\DnvScore\\comp_all_parts", // "C:\\Work\\msms5\\DnvScore\\short2_train_mgf_list.txt", "C:\\Work\\msms5\\DnvScore\\comp2_train_mgf_list.txt", 2, 1, 30000, 5); // model.read_model("ETD"); // config = model.get_config(); // config->apply_selected_PTMs("M+16:Q-17:N+1:C+57"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\PepNovoHQ\\ETD2\\ETD_unique_train.txt"); // model.full_train_model("ETD",fm,0.5); // model.train_pmc_rank_models("C:\\Work\\msms5\\PepNovoHQ\\ETD2\\ETD_all_train.txt"); // model.write_model(); exit(0); // train_all(); // create_training_sets(); // exit(0); // generate_size_reports(); // test_sims(); // data_set_stats(); // convert_list_to_trianing_peptide_file( // "C:\\Work\\msms5\\NewScore\\lists\\Dicty_98_3_unique_mgf_list.txt", // "C:\\Work\\msms5\\NewScore\\tps\\Dicty_98_3_unique_tps.txt"); // proline_cleavage_reports("b",2); // exit(0); // center_cleavage_reports("y",3); // n_terminal_cleavage_reports("y",2); // c_terminal_cleavage_reports("y",-2); // find_best_similar_pairs("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf",8); // find_self_similarity("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf"); // find_similar_pairs_ditrib("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf"); // find_homeometric_similarity_distrib("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf"); // find_self_similarity_ranges("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\SHEW18.mgf"); // peptide_distances(); // find_matches_similarity_distrib("LTQ_LOW_TRYP", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf", // "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf"); // match_sim_exp(); // exit(0); // edge_model.train_all_edge_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2); // saa.train_saa_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2); // saa.train_saancd_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2); // daa.train_daa_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2,0.25); // daa.train_daancd_model("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2); // dot_prod_exp(); // qc_exp(); // qc_ann_exp("64068",true); // exit(0); config = model.get_config(); config->init_with_defaults(); config->apply_selected_PTMs("M+16:Q-17:N+1:C+57"); fm.init_from_file(config,"C:\\Work\\msms5\\PepNovoHQ\\ETD\\train_etd.mgf"); model.full_train_model("ETD",fm,0.5); exit(0); if (1) { model.read_model("LTQ_LOW_TRYP"); // model.get_config()->apply_selected_PTMs("C+57:M+16"); // model.get_config()->init_with_defaults(); model.get_config()->apply_selected_PTMs("M+16:C+57:Q-17"); // model.test_pmc("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\sqs_train_1.mgf",1); // model.compute_sqs_cum_stats_for_ided("C:\\Work\\msms5\\NewScore\\lists\\all_HEK_mgf_list.txt"); // model.compute_sqs_cum_stats_for_crap("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\crap_list.txt"); // model.write_model(); model.compute_sqs_cum_stats_for_ided("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40good\\H40good_mgf_list.txt"); /// model.benchmark_sqs("C:\\Work\\msms5\\PepNovoHQ\\small_list.txt", // "C:\\Work\\msms5\\PepNovoHQ\\small_anns.txt"); // model.benchmark_sqs("C:\\Work\\msms5\\PepNovoHQ\\tmp\\H40ul_0_list.txt", // "C:\\Work\\msms5\\PepNovoHQ\\H40ul55_missed.txt"); // "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40ul98_anns.txt"); exit(0); DAT_Converter dat; dat.create_dat_files_for_anns(model.get_config(), "C:\\Work\\Data\\Briggs\\HEK293\\40ul_list.txt", // "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40ul98_anns.txt", "C:\\Work\\msms5\\PepNovoHQ\\H40ul55_missed.txt", "C:\\Work\\msms5\\PepNovoHQ\\tmp\\", "H4055"); // // model.train_pmc_rank_models( // "C:\\Work\\msms5\\NewScore\\lists\\HEK_98_1_unique_mgf_list.txt",0); // "C:\\Work\\msms5\\NewScore\\lists\\all_unique_mgf_list.txt",0); // "C:\\Work\\msms5\\NewScore\\lists\\all_HEK_mgf_list.txt",0); // model.write_model(); // make_before_and_after_matrices(model.get_config(),"C:\\Work\\msms5\\lists\\mgf10.txt",3,"y"); exit(0); FileManager fm; fm.init_from_list_file(model.get_config(),"C:\\Work\\msms5\\lists\\LTQ_train_list.txt"); model.full_train_model("LTQ_IT_TRYP",fm,0.45); model.write_model(); // model.train_pmc("C:\\Work\\msms5\\lists\\pos_sqs_list.txt"); vector< vector<float> > weights; weights.resize(4); weights[1].resize(3,0); weights[2].resize(3,0); weights[3].resize(3,0); weights[1][0] = 0.1; weights[1][1] = 0.1; weights[1][2] = 0.4; weights[2][0] = 0.6; weights[2][1] = 0.75; weights[2][2] = 0.5; weights[3][0] = 0.3; weights[3][1] = 0.15; weights[3][2] = 0.1; // model.train_sqs("C:\\Work\\msms5\\lists\\pos_sqs_list.txt", // "C:\\Work\\msms5\\lists\\neg_sqs_list.txt",&weights); // model.train_sqs("C:\\Work\\msms5\\NewScore\\lists\\all_unique_mgf_list.txt", // "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\crap_list.txt",&weights); // config = model.get_config(); // config->set_tolerance(0.5); // // find_pair_similarities(config,"C:/Work/clust_exp/Results/Shew_bm/ShewBM40_0_1.mgf", // "C:/Work/clust_exp/Results/Shew_bm/ShewBM40_pairs.txt"); exit(0); } // make_y_vectors("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\sqs10_train_2.mgf",&model); // create_training_files(config); // exit(0); if (0) { PMCSQS_Scorer sqs; // exit(0); // create_training_files(config); exit(0); } if (1) { // fm.init_from_file(model.get_config(),"C:\\Work\\msms5\\PepNovoHQ\\orbi_ann.mgf"); // create_MSB_query_for_file_list(fm,&model); vector< vector<int> > annotation_idxs; vector<mzXML_annotation> annotations; read_mzXML_annotations("C:/Work/Data/Briggs/HEK293_mzxml_list.txt", "C:/Work/ClusterAnn/mzxml_anns3.txt", annotation_idxs, annotations, 35000); // read_mzXML_annotations("C:/Work/ClusterAnn/H40ul_mgf_list.txt", // "C:/Work/ClusterAnn/mgf_anns.txt", annotation_idxs, annotations, 35000); cout << "Read annotations: " << annotations.size() << endl; fm.init_from_list_file_and_add_annotations(config,"C:/Work/Data/Briggs/HEK293_mzxml_list.txt", annotation_idxs, annotations,true); // fm.init_from_list_file_and_add_annotations(config,"C:/Work/ClusterAnn/H40ul_mgf_list.txt",annotation_idxs, // annotations,true); FileSet all_spec_fs; all_spec_fs.select_all_files(fm,true); // config->set_need_to_normalize(0); // all_spec_fs.create_MGF_file(fm,config,"C:/Work/ClusterAnn/mgf_spectra.mgf"); // exit(0); ofstream mgf_stream("C:/Work/ClusterAnn/mzxml_spectra3.mgf",ios::out); BasicSpecReader bsr; const vector<SingleSpectrumFile *>& ssfs = all_spec_fs.get_ssf_pointers(); int i; for (i=0; i<ssfs.size(); i++) { static QCPeak peaks[5000]; BasicSpectrum bs; MZXML_single *ssf = (MZXML_single *)ssfs[i]; bs.peaks = peaks; bs.ssf = ssf; ostringstream oss; oss << ssf->file_idx << " " << ssf->scan_number; ssf->single_name = oss.str(); bs.num_peaks = bsr.read_basic_spec(config,fm,ssf,peaks); if (ssf->scan_number<0) { cout << "Error: no scan number read from mzXML!!!" << endl; exit(1); } cout << "scan: " << ssf->scan_number << " " << bs.num_peaks << endl; bs.output_to_mgf(mgf_stream,config); // bs.output_to_mgf(cout,&config); } //all_spec_fs.create_MGF_file(fm,config,"C:/Work/ClusterAnn/mzxml_spectra.mgf"); // extractMZFromFiles(model.get_config(),,"C:/Work/Data/Briggs/HEK293/H29340ul_mz.txt"); // exit(0); } if (1) { model.read_model("LTQ_LOW_TRYP"); config = model.get_config(); config->apply_selected_PTMs("C+57 M+16"); config->set_tolerances(0.5); config->set_pm_tolerance(2.5); config->set_digest_type(TRYPSIN_DIGEST); config->set_max_number_peaks_per_local_window(15); // fm.init_from_list_file(config,"C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\LTQ_train_list.txt"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\orbi_train.txt"); // edge_model.train_all_edge_models(fm,&model); // tm.train_models(fm,&model); // fm.init_from_list_file(config,"C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt"); // make_frag_rank_histogram(fm,config); // exit(0); // benchmark_k_value(config,"C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt"); // make_benchmark_clustering_dataset(config, "C:\\Work\\clust_exp\\ShewMGF\\AnnsPlus_ann_list.txt", // 600, 750, false, "C:\\Work\\clust_exp\\ShewMGF\\", "BMNEW"); // exit(0); benchmark_clustering_performance(config, "C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt",15); // print_dataset_spectra_by_stats(config,"C:\\Work\\clust_exp\\ann_mgf\\Sings_1.mgf"); // benchmark_top7_and_sim_thresh(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt", // "C:\\Work\\clust_exp\\Results\\BM40ul\\BM40ul_anns.txt"); // benchmark_heuristic_filtering(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt"); // benchmark_retention_thresh(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt", // "C:\\Work\\clust_exp\\Results\\BM40ul\\BM40ul_anns.txt"); exit(0); FileManager fm; // fm.init_from_mgf(config,"C:\\Work\\clust_exp\\ShewMGF\\OnlyAnn_1.mgf"); // make_specified_benchmark_clustering_dataset(config,"C:\\Work\\clust_exp\\ShewMGF\\both_list.txt",400,1000, // "C:\\Work\\clust_exp\\ShewMGF\\","BM3000",3000,10,0); make_benchmark_clustering_dataset(config, "C:\\Work\\clust_exp\\ShewMGF\\AnnsPlus_ann_list.txt", 800, 1200, true, "C:\\Work\\clust_exp\\ShewMGF\\", "AnnOnly"); exit(0); ann_mgf_and_create_mgf_with_sim_masses(config,"K:\\Work\\Data\\Shewenella\\FT_anns.txt", "K:\\Work\\Data\\Shewenella\\FT_mgf_list.txt", "K:\\Work\\Data\\Shewenella\\FT_peptides.txt", "C:\\Work\\clust_exp\\ShewMGF\\", "AnnsPlus"); exit(0); ann_mgf_and_create_mgf(config,"C:\\Work\\Data\\FT_mgf\\FT_single_anns.txt", "C:\\Work\\Data\\FT_mgf\\FT_single_mgf.txt", "C:\\Work\\clust_exp\\ShewMGF\\", "Single",true); exit(0); ann_mgf_and_create_mgf(config,"C:\\Work\\Data\\FT_mgf\\FT_anns.txt", "C:\\Work\\Data\\FT_mgf\\FT_mgf_list.txt", "C:\\Work\\clust_exp\\ShewMGF\\", "OnlyAnn",true); exit(0); // create_16O_18O_dataset("C:\\Work\\msms5\\lists\\p19_list.txt",config); // exit(0); // config->set_need_to_estimate_pm(0); model.clone_charge_model(2,1); model.clone_charge_model(2,3); model.clone_charge_model(2,4); model.clone_charge_model(2,5); // dataset_eval(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.05); // dataset_eval(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1); // dataset_eval(&model,"C:\\Work\\msms5\\lists\\list280_mgf.txt",0.6); vector<int> set_sizes; vector<float> probs; denovo_sequencing_and_aa_probs(&model,"C:\\Work\\msms5\\lists\\m280_list.txt", set_sizes,probs,2); // denovo_sequencing_and_aa_probs(&model,"C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt", // set_sizes,probs,2); // // output_denovo_results(&model,"C:\\Work\\msms5\\lists\\LTQ-FT_mgf_list.txt"); // denovo_sequencing_and_aa_probs(&model,"C:\\Work\\msms5\\lists\\LTQ-FT_mgf_list.txt", // set_sizes,probs, 2); exit(0); // print_specs(model.get_config(), "C:\\Work\\msms5\\lists\\one_mzxml.txt"); // check_m_over_z(&model,"C:\\Work\\msms5\\lists\\CoCl345sann_ann_list.txt"); // calc_parent_mass_tolerance_distribution(&model, "C:\\Work\\msms5\\lists\\ann_mgf_list.txt" , 0.6, 0.98); // calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_mgf_list.txt", 0.6, 0.95); // perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_mgf_list.txt",0.5,2,0.05); // denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt" ,0.0075); // denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1); // denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.008); // perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.2,2,0.05); // perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.025,2,0.05); // calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1,0.95); // calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.1,0.95); // calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.1,0.95); // calc_tolerance_distribution(&model,"C:\\Work\\Data\\Omics04\\omics_ann_list.txt",0.75,0.95); // calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1,0.975); // calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.1,0.975); // calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.1,0.975); exit(0); // fm.init_from_mgf(config,"C:\\Work\\msms4\\PepNovo\\test\\m280.mgf"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\good_list2.txt"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\p215.txt"); // fm.init_from_list_file(config,"C:\\Work\\Data\\Omics04\\omics_ann_list.txt"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\omics_mgf_list.txt"); // fm.init_from_mgf(config,"C:\\Work\\msms5\\PepNovoHQ\\Omics04Spectra.mgf"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\omics02_dta.txt"); // FileSet fs; // fs.select_all_files(fm); // fs.sort_according_to_m_over_z(); // fs.create_MGF_file(fm,config,"Omics02Spectra.mgf"); // exit(0); // collect_denovo_statistics(fm,&model); // denovo_histograms(fm,&model); // config->set_tolerance(0.0075); // random_check_homemorphic(config,50000,25); // create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\Drosophila_list.txt",".","cc",0,5E6,0,1E6); // create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\Dros_short.txt",".","cc",0,1E6,0,1E6); // create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\all_clust.txt","clust_out","ikkb",0,5E6,0,1E6); // create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\omics_mgf_list.txt","clust_out", // "Omics04b",0,5E6,0,1E6); // create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\omics02_mgf_list.txt","clust_out", // "Omics02",0,5E6,0,1E6); // create_spectrum_clusters(config,"C:\\Work\\msms5\\PepNovoHQ\\clust_out2\\h293_dat_list.txt", // "clust_out2","H293b_2nd_digest_abd3",0,5E6,1938.76,1E6,2); // create_spectrum_clusters(config,"C:\\Work\\msms5\\PepNovoHQ\\clust_out\\h29s_list.txt","clust_out", // "xxxx",0,5E6,835.397,1E6,2); exit(0); DAT_Converter dat; dat.init_DAT_Converter(2000,25,1048576); exit(0); } // config->add_selected_PTMs("C+57 M+16 S+80 T+80 Y+80 N+1 Q+1 K+42 D+16 K+16 P+16 N+16"); // config->set_tolerances(0.0075); // config->set_pm_tolerance(0.011); // fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\contaminants.fasta",config); // fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\Homo_sapiens.NCBI35.dec.pep.fa",config); // fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa50mb.fa",config,true,5,6); // fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\homo_pos.fa",config); // fdb.print_protein_names(); // fdb.write_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\h**o.dat"); // fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\h**o.dat",config); // fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\qqq.dat",config); // fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa500k.dat",config); // fdb.print_protein_names(); // fdb.write_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa5--0mb.dat"); // exit(0); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_seq_list.txt"); // fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_u_list.txt"); fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_376.txt"); // make_bin_histograms(fm,config); // calc_avg_rand(fm,config); // explore_fragment_set(fm,config); // show_occurences(fm,config,"p-25.0"); // find_internal_offset_counts(fm,config); // make_frag_rank_histogram(fm,config); // exit(0); // internal_fragment_annotation(fm,model.get_config()); // find_internal_offset_counts(fm,model.get_config()); // exit(0); FileSet fs; fs.select_all_files(fm); fstream ofs("true_seq.txt",ios::out); fs.make_fasta_from_file_seqs(fm,config,45,ofs); // dbsm.train_regression_models(fm,fdb,12,&model); // analyze_cad_spec(fm,config); // make_rank_histograms(fm,&model); // dbsm.read_model("DBS.txt"); // CAD_histograms(fm,&model,fdb,&dbsm); // rand_db_stats(fm,&model,&dbsm); // db_search_stats(fm,&model,&dbsm); // neg_db_search_stats(fm,&model,&dbsm); // CAD_edge_stats(fm,&model); // CAD_denovo_histograms(fm,&model,fdb); // CAD_edge_stats(fm,&model); // collect_denovo_statistics(fm,&model); exit(0); // int *arr; // int t_size; // read_fasta("cshort.fasta",&arr,&t_size,&config); // read_fasta("C:\\Work\\msms4\\PepNovo\\Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config); // homeomorphic_levels(&config,arr,t_size,1000.0,1001,"hp_res.txt"); config->set_tolerance(0.0075); // full_exp(config,0,arr,t_size,"hp_res_dis_a0.txt"); // full_exp(config,1,arr,t_size,"hp_res_dis_a1.txt"); // full_exp(config,2,arr,t_size,"hp_res_dis_a2.txt"); // full_exp(config,3,arr,t_size,"hp_res_dis_a3.txt"); // full_exp(config,4,arr,t_size,"hp_res_dis_a4.txt"); // homeomorphic_exp3(&config,100); // exit(0); // config.print_supported_PTMs(); // config.print_session_aas(); string p; // ifstream fs("D:\\msms4\\PepNovo\\test\\C25A19_IP_01.mgf",ios::in); // ifstream fs("D:\\msms4\\PepNovo\\test\\m280.mgf",ios::in); // fm.init_from_mgf(&config,"D:\\msms4\\PepNovo\\test\\m280.mgf"); // fm.init_from_mgf(&config,"D:\\msms4\\PepNovo\\mgf_2600.2.mgf"); // fm.init_from_list_file(&config,"D:\\msms4\\lists\\unique_good2.txt"); // fm.init_from_list_file(&config,"D:\\msms4\\lists\\short2.txt"); // fm.init_from_list_file(&config,"D:\\Data2\\ikkb_unmod_list.txt"); // rand_seed(1111); rand_seed(1426347); // model.read_model("ESI_RANKS"); // model.get_config()->add_selected_PTMs("C+57"); // SpectrumScore sqs; // sqs.learn_score_params(&model,"D:\\msms4\\lists\\sqs2_short.txt", // "D:\\msms4\\lists\\sqs_neg1.txt"); // exit(0); // model.set_model_name(string("ESI2")); // random_peak_match_exp(model.get_config(),fm,800,1200,10000000); // model.print_joint_scores(); // me_reg_exp(); // me_exp(); // exit(0); // fm.init_from_mgf(model.get_config(),"c:\\work\\msms4\\PepNovo\\test\\m280.mgf"); // fm.init_from_mgf(model.get_config(),"c:\\work\\msms4\\PepNovo\\hpep.mgf"); fm.init_from_list_file(config,"c:\\Work\\msms4\\lists\\efast2.txt"); // fm.init_from_list_file(&config,"D:\\msms4\\lists\\charge2.txt"); //m.init_from_list_file(model.get_config(),"C:\\Work\\msms4\\PepNovo\\lll.txt"); //m.init_from_list_file(model.get_config(),"D:\\msms4\\lists\\l1.txt"); */ return 0; }