Index

A

add_Edge() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorModel_Parms method) add_realization() (pygor3.IgorIO.IgorRec_Event method) AIRR_gene (class in pygor3.AIRR) AIRR_VDJ_rearrangement (class in pygor3.AIRR) align() (pygor3.IgorIO.IgorTask method)

appendList_IgorAlignments_data_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) attach_anchors_from_files() (pygor3.IgorIO.IgorModel_Parms method) attach_J_anchors_from_file() (pygor3.IgorIO.IgorModel_Parms method) attach_table_from_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) attach_V_anchors_from_Dataframe() (pygor3.IgorIO.IgorModel_Parms method) attach_V_anchors_from_file() (pygor3.IgorIO.IgorModel_Parms method)

C

calc_average() (in module pygor3.scripts.observable) (in module pygor3.scripts.scriptTest) calc_IgorBestScenarios_average_of() (pygor3.IgorSqliteDB.IgorSqliteDB method) calc_IgorBestScenarios_sum_of() (pygor3.IgorSqliteDB.IgorSqliteDB method) clean_empty_anchors() (pygor3.IgorIO.IgorRefGenome method) close_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) command_from_dict_options() (in module pygor3.IgorIO) connect_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) construct_sequence_VDJ_from_realization_dict() (pygor3.IgorIO.IgorModel method) construct_sequence_VJ_from_realization_dict() (pygor3.IgorIO.IgorModel method)

copytable_from_source() (pygor3.IgorSqliteDB.IgorSqliteDB method) create_config_files() (in module pygor3.config) create_connection() (in module pygor3.IgorIndexedSequencesDB) create_db() (pygor3.IgorIO.IgorTask method) (pygor3.IgorSqliteDB.IgorSqliteDB class method) create_table() (in module pygor3.IgorIndexedSequencesDB) create_table_sql (in module pygor3.IgorIndexedSequencesDB) createSqliteDB() (pygor3.IgorSqliteDB.IgorSqliteDB method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) createSqliteDB_tmp() (pygor3.IgorSqliteDB.IgorSqliteDB method)

D

D (pygor3.IgorIO.IgorRefGenome property) db_export_IgorGenomes() (pygor3.IgorIO.IgorTask method) db_export_IgorIndexedSeq() (pygor3.IgorIO.IgorTask method) db_export_to_igorfiles() (pygor3.IgorIO.IgorTask method) db_get_naive_align_dict_by_seq_index() (pygor3.IgorIO.IgorTask method) db_ls() (pygor3.IgorIO.IgorTask method) db_plot_naive_align_by_seq_index() (pygor3.IgorIO.IgorTask method) db_str_fasta_naive_align_by_seq_index() (pygor3.IgorIO.IgorTask method) default_model() (pygor3.IgorIO.IgorTask class method) delete_IgorAlignments_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorBestScenarios_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorGeneAnchors_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorGeneTemplate_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorIndexedCDR3_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorIndexedSeq_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorModel_Marginals_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorModel_Parms_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorModel_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) delete_IgorPgen_Tables() (pygor3.IgorSqliteDB.IgorSqliteDB method)

DEV_from_df_scenario_aln_to_da_scenario_aln_complete_genes() (in module pygor3.utils) df_D_ref_genome (pygor3.IgorIO.IgorModel_Parms property) df_J_ref_genome (pygor3.IgorIO.IgorModel_Parms property) (pygor3.IgorIO.IgorRefGenome property) df_V_ref_genome (pygor3.IgorIO.IgorModel_Parms property) (pygor3.IgorIO.IgorRefGenome property) dict_genomicDs (pygor3.IgorIO.IgorRefGenome property) dict_genomicJs (pygor3.IgorIO.IgorRefGenome property) dict_genomicVs (pygor3.IgorIO.IgorRefGenome property) dna_complementary() (in module pygor3.utils) dna_translate() (in module pygor3.utils) download_gene_template() (in module pygor3.imgt) download_genes_anchors() (in module pygor3.imgt) download_Jgene_anchors() (in module pygor3.imgt) download_ref_genome() (in module pygor3.imgt) download_ref_genome_VDJ() (in module pygor3.imgt) download_ref_genome_VJ() (in module pygor3.imgt) download_Vgene_anchors() (in module pygor3.imgt) download_Vgene_anchors_bk() (in module pygor3.imgt) ds_SONIA_model() (in module pygor3.IgorIO)

E

ErrorRate_dict (pygor3.IgorIO.IgorModel property) evaluate() (in module pygor3.IgorIO) (pygor3.IgorIO.IgorTask method) evaluate_pgen() (in module pygor3.IgorIO) event_Deletion_list (pygor3.IgorIO.IgorModel_Parms property) event_Deletion_nickname_list (pygor3.IgorIO.IgorModel property) event_DinucMarkov_list (pygor3.IgorIO.IgorModel_Parms property) event_DinucMarkov_nickname_list (pygor3.IgorIO.IgorModel property) event_GeneChoice_D (pygor3.IgorIO.IgorModel_Parms property) event_GeneChoice_D_nickname (pygor3.IgorIO.IgorModel property) event_GeneChoice_J (pygor3.IgorIO.IgorModel_Parms property) event_GeneChoice_J_nickname (pygor3.IgorIO.IgorModel property) event_GeneChoice_list (pygor3.IgorIO.IgorModel_Parms property) event_GeneChoice_nickname_list (pygor3.IgorIO.IgorModel property) event_GeneChoice_V (pygor3.IgorIO.IgorModel_Parms property) event_GeneChoice_V_nickname (pygor3.IgorIO.IgorModel property) event_Insertion_list (pygor3.IgorIO.IgorModel_Parms property)

event_Insertion_nickname_list (pygor3.IgorIO.IgorModel property) execute_command_generator() (in module pygor3.IgorIO) execute_query() (pygor3.IgorSqliteDB.IgorSqliteDB method) execute_select_query() (pygor3.IgorSqliteDB.IgorSqliteDB method) execute_select_query_fetchone() (pygor3.IgorSqliteDB.IgorSqliteDB method) executescript() (pygor3.IgorSqliteDB.IgorSqliteDB method) export_csv() (pygor3.IgorIO.IgorModel method) export_event_to_csv() (pygor3.IgorIO.IgorModel method) export_IgorBestScenarios_to_AIRR() (pygor3.IgorSqliteDB.IgorSqliteDB method) export_model() (pygor3.IgorIO.IgorModel method) export_plot_events() (pygor3.IgorIO.IgorModel method) export_plot_Pconditionals() (pygor3.IgorIO.IgorModel method) export_plot_Pmarginals() (pygor3.IgorIO.IgorModel method) export_Pmarginal_to_csv() (pygor3.IgorIO.IgorModel method) export_realizations_to_fasta() (pygor3.IgorIO.IgorRec_Event method) export_to_AIRR_line() (pygor3.IgorIO.IgorScenario method) extract_fasta_from_url() (in module pygor3.imgt)

F

fetch_AIRR_arrangement_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_best_IgorAlignments_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorAlignments_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorAlignments_By_seq_index_and_gene_name() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorBestScenarios_By_events_dict() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorBestScenarios_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorBestScenariosVDJ_By_seq_index() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) fetch_IgorGeneAnchors_By_Gene() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorGeneTemplate_By_gene_id() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorGeneTemplate_By_gene_name() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorGenomicData_By_Gene() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorIndexedCDR3_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorIndexedSeq_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorIndexedSeq_By_seq_indexList() (pygor3.IgorSqliteDB.IgorSqliteDB method)

fetch_IgorIndexedSeq_indexes() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorIndexedSeq_records() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorPgen() (pygor3.IgorSqliteDB.IgorSqliteDB method) fetch_IgorPgen_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) FIXME_calc_IgorBestScenarios_average_of() (pygor3.IgorSqliteDB.IgorSqliteDB method) from_database() (pygor3.IgorIO.IgorModel_Parms class method) from_default_nickname() (pygor3.IgorIO.IgorRec_Event class method) from_df_scenario_aln_to_da_scenario_aln() (in module pygor3.utils) from_dict() (pygor3.IgorIO.IgorEvent_realization class method) (pygor3.IgorIO.IgorRec_Event class method) from_network_dict() (pygor3.IgorIO.IgorModel_Parms class method) from_pandas() (pygor3.IgorIO.IgorEvent_realization class method) from_scenario() (pygor3.IgorIO.IgorModel_Parms method) from_tuple() (pygor3.IgorIO.IgorEvent_realization class method)

G

gen_EventDict_DataFrame() (pygor3.IgorIO.IgorModel_Parms method) gen_igor_wd() (pygor3.IgorIO.IgorTask method) gen_IgorBestScenarios_cols_list() (pygor3.IgorSqliteDB.IgorSqliteDB method) gen_NameNickname_dict() (pygor3.IgorIO.IgorModel_Parms method) gen_random_batchname() (pygor3.IgorIO.IgorTask method) gen_short_names() (in module pygor3.imgt) genAnchDict() (in module pygor3.imgt) generate() (in module pygor3.IgorIO) (pygor3.IgorIO.IgorTask method) generate_csv_line() (in module pygor3.scripts.naive_align) (in module pygor3.scripts.naive_align_id) generate_event_delta_Kronecker() (in module pygor3.scripts.observable) (in module pygor3.scripts.scriptTest) generate_Pmarginals() (pygor3.IgorIO.IgorModel method) generate_sequence_construction_list() (pygor3.IgorIO.IgorModel method) generate_str_fasta() (in module pygor3.scripts.all_gene_alignments_id) (in module pygor3.scripts.naive_align_id) generate_str_fasta_simple() (in module pygor3.scripts.naive_align) (in module pygor3.scripts.naive_align_id) generate_xdata() (pygor3.IgorIO.IgorModel method) GeneSegment (class in pygor3.utils) genKey() (in module pygor3.imgt) genLabel() (in module pygor3.IgorIO) genMarginalFile() (pygor3.IgorIO.IgorModel_Parms method) genPreMarginalDF() (pygor3.IgorIO.IgorModel_Parms method) get_AIRR_from_ps_scenario() (pygor3.IgorIO.IgorModel method) get_AIRR_VDJ_rearragement_dict_from_scenario() (pygor3.IgorIO.IgorModel method) get_AIRR_VJ_rearragement_dict_from_scenario() (pygor3.IgorIO.IgorModel method) get_aln_scenario_np_from_da_scenario_aln() (in module pygor3.utils) get_anchors_dataframe_from_csv() (in module pygor3.utils) get_anchors_dict() (pygor3.IgorIO.IgorRefGenome method) get_best_IgorAlignment_data_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_BestScenariosDataFrame() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) get_BestScenariosNaiveSeq() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) get_CDR3_data() (in module pygor3.scripts.scriptTest02) get_CDR3_nt_pos_from_ps_scenario() (pygor3.IgorIO.IgorModel method) get_CDR3_VJ_anchors() (in module pygor3.IgorIO) get_colors() (in module pygor3.utils) get_columns_type_of_tables() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_conditional_entropy_dinucl_function_l_ins() (pygor3.IgorIO.IgorModel method) get_cross_entropy() (pygor3.IgorIO.IgorModel static method) get_D_KL_from_xarray() (in module pygor3.utils) get_da_clustalw_align_from() (in module pygor3.utils) get_dataframe_from_fasta() (in module pygor3.utils) get_dataframe_from_fasta_and_csv_anchors() (in module pygor3.utils) get_dataframe_from_fln_generated_realizations_werr() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorTask method) get_dataframe_from_fln_generated_seqs_werr() (in module pygor3.utils) (pygor3.IgorIO.IgorTask method) get_DataFrame_IgorAlignment_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_dataframe_scenarios() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorTask method) get_dataframe_with_ref_genome_column_names() (in module pygor3.utils) get_default_fln_dict_ref_genomes_species_chain() (in module pygor3.utils) get_default_fln_names_for_model_dir() (in module pygor3.utils) get_default_IgorModel() (in module pygor3.IgorIO) get_default_models_fln_paths() (in module pygor3.utils) get_default_models_paths_species_chain() (in module pygor3.utils) get_default_ref_genome_fln_paths() (in module pygor3.utils) get_df_anchors_from_df_ref_genome() (in module pygor3.utils) get_df_Deletion_entropy_contribution() (pygor3.IgorIO.IgorModel method) get_df_entropy_decomposition() (pygor3.IgorIO.IgorModel method) get_df_events_rearrangement() (pygor3.IgorIO.IgorModel method) get_df_GeneChoice_entropy_contribution() (pygor3.IgorIO.IgorModel method) get_df_Insertion_entropy_contribution() (pygor3.IgorIO.IgorModel method) get_df_normalize_prob() (in module pygor3.utils) (pygor3.IgorIO.IgorModel static method) get_df_order_cols_ref_genome() (in module pygor3.utils) get_df_pgen() (in module pygor3.utils) get_df_realizations() (pygor3.IgorIO.IgorModel method) get_df_realizations_dinucl() (pygor3.IgorIO.IgorModel method) get_df_scenario_aln_from_scenario() (pygor3.IgorIO.IgorModel method) get_dict_from_imgt_description() (in module pygor3.imgt) get_dict_of_Igortablename_sql() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_DictNicknameProbs() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) get_Edges() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_entropy_event() (pygor3.IgorIO.IgorModel method) get_ErrorProb() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) get_ErrorRate_dict() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_Event() (pygor3.IgorIO.IgorModel_Parms method) get_Event_dependencies() (pygor3.IgorIO.IgorModel_Parms method) get_event_dict() (pygor3.IgorIO.IgorModel_Parms method) get_Event_list() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_Event_list_sorted() (pygor3.IgorIO.IgorModel_Parms method) get_Event_Marginal() (pygor3.IgorIO.IgorModel method) get_Event_realization() (pygor3.IgorIO.IgorModel_Parms method) get_event_realization_of_event() (pygor3.IgorIO.IgorModel method) get_event_realizations_DataFrame() (pygor3.IgorIO.IgorModel method) get_Event_value() (pygor3.IgorIO.IgorModel method) get_EventProb() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) get_events_nicknames_list() (pygor3.IgorIO.IgorModel method) get_events_types_list() (pygor3.IgorIO.IgorModel method) get_EventsName_list() (pygor3.IgorIO.IgorModel_Parms method) get_EventsNickname_list() (pygor3.IgorIO.IgorModel_Parms method) get_gene_anchors() (in module pygor3.imgt) get_gene_segment() (in module pygor3.utils) get_gene_segment_dict() (pygor3.IgorIO.IgorModel method) get_gene_template() (in module pygor3.imgt) get_genedb_query72() (in module pygor3.imgt) get_genedb_query81_imgtlabel() (in module pygor3.imgt) get_IgorAlignment_data_list_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorAlignment_data_list_query() (pygor3.IgorSqliteDB.IgorSqliteDB method)

get_IgorBestScenarios_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorBestScenarios_By_seq_index_IgorModel() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorBestScenariosDataframe_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorEvent_realization() (pygor3.IgorIO.IgorModel method) get_IgorEvent_realization_for_nickname() (pygor3.IgorIO.IgorModel method) get_IgorGenomicDataFrame_dict() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorIndexedSeq_By_seq_index() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorModel() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorModel_from_IgorRefGenome() (in module pygor3.IgorIO) get_IgorModel_Marginals() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorModel_Parms() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_IgorRefGenome() (pygor3.IgorIO.IgorModel_Parms method) get_IgorRefGenome_VDJ_from_IMGT() (in module pygor3.IgorIO) get_IgorRefGenome_VJ_from_IMGT() (in module pygor3.IgorIO) get_imgt_list_species() (in module pygor3.IgorIO) (pygor3.IgorIO.IgorRefGenome static method) get_join_genomics_anchors_dataframes() (in module pygor3.utils) get_list_of_tables_with_name() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_mutual_information() (pygor3.IgorIO.IgorModel method) get_mutual_information_events() (pygor3.IgorIO.IgorModel method) get_mutual_information_events_from_df_scenarios() (pygor3.IgorIO.IgorModel method) get_mutual_information_from_df_scenarios() (pygor3.IgorIO.IgorModel method) get_naive_sequence_from_IgorAligment_data() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_nicknames_for_gene_segment() (pygor3.IgorIO.IgorModel method) get_observable_from_df_scenarios() (pygor3.IgorIO.IgorModel method) get_observable_xarray_from_function() (pygor3.IgorIO.IgorModel method) get_ones_xarray_from_list() (pygor3.IgorIO.IgorModel method) get_P_from_scenarios_cols() (pygor3.IgorIO.IgorModel method) get_P_joint() (pygor3.IgorIO.IgorModel method) get_P_marginal_from_df_scenarios_cols() (pygor3.IgorIO.IgorModel method) get_P_stationary_state_dinucl() (in module pygor3.utils) get_pairwise_prob() (in module pygor3.scripts.bs_pairwise_prob) (in module pygor3.scripts.scriptTest) get_pgen_pd() (pygor3.IgorIO.IgorTask method) get_probability_matrix_from_event_list_and_scenarios_dataframe() (pygor3.IgorIO.IgorModel method) get_realization() (pygor3.IgorIO.IgorRec_Event method) get_realization_DataFrame() (pygor3.IgorIO.IgorRec_Event method) get_realization_value_from_df_scenarios() (pygor3.IgorIO.IgorModel method) get_realization_vector() (pygor3.IgorIO.IgorRec_Event method) get_realizations_dict_from_scenario_dict() (pygor3.IgorIO.IgorModel method) get_records_list() (in module pygor3.imgt) get_ref_genome_dataframe_from() (in module pygor3.utils) get_scenario_fasta() (pygor3.IgorIO.IgorScenario method) get_scenario_from_line_CSV() (pygor3.IgorIO.IgorModel_Parms method) get_sequence() (pygor3.IgorIO.IgorGeneTemplate method) get_sonia_input() (in module pygor3.IgorIO) get_sorted_events_nicknames_list() (pygor3.IgorIO.IgorModel method) get_species_list() (in module pygor3.imgt) get_str_seq_from_ps_scenario() (pygor3.IgorIO.IgorModel method) get_table_colsname_list() (pygor3.IgorSqliteDB.IgorSqliteDB method) get_V_anchor_index_in_seq_from_gene() (in module pygor3.scripts.all_gene_alignments_id) get_VDJ_CDR3_from_df_scenario() (pygor3.IgorIO.IgorModel method) get_VDJ_CDR3_from_scenario() (pygor3.IgorIO.IgorModel method) get_zero_xarray_from_list() (pygor3.IgorIO.IgorModel method) getBayesGraph() (pygor3.IgorIO.IgorModel_Parms method) getD_3_dels() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getD_5_dels() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getD_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getD_gene_name() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getD_ntsequence() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getD_Region() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) getDJ_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getDJ_ins() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getDJ_Region() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) getFunction() (in module pygor3.imgt) getJ_5_dels() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getJ_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getJ_gene_name() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getJ_ntsequence() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getJ_Region() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) getStartPos() (in module pygor3.imgt) getV_3_dels() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getV_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getV_gene_name() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getV_ntsequence() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getV_Region() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) getVD_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getVD_ins() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) getVD_Region() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method)

I

id (pygor3.IgorIO.IgorEvent_realization attribute) Igor_dict_order_seq_side (in module pygor3.IgorDefaults) IgorAlignment_data (class in pygor3.IgorIO) IgorAnchors (class in pygor3.IgorIO) IgorBestScenariosVDJ (class in pygor3.IgorBestScenarios) (class in pygor3.IgorIO) IgorEvent_realization (class in pygor3.IgorIO) IgorGeneTemplate (class in pygor3.IgorIO) IgorIndexedSequence (class in pygor3.IgorIndexedSequence) (class in pygor3.IgorIO) IgorIndexedSequencesDB (class in pygor3.IgorIndexedSequencesDB) IgorModel (class in pygor3.IgorIO) IgorModel_Marginals (class in pygor3.IgorIO) IgorModel_Parms (class in pygor3.IgorIO) IgorRec_Event (class in pygor3.IgorIO) IgorRefGenome (class in pygor3.IgorIO) IgorScenario (class in pygor3.IgorIO) IgorSqliteDB (class in pygor3.IgorSqliteDB) IgorSqliteDBBestScenariosVDJ (class in pygor3.IgorSqliteDBBestScenarios)

IgorTask (class in pygor3.IgorIO) infer() (in module pygor3.IgorIO) (pygor3.IgorIO.IgorTask method) infer_SONIA_from_directory() (in module pygor3.IgorIO) initialize_uniform_event_from_model_parms() (pygor3.IgorIO.IgorModel_Marginals method) initialize_uniform_from_model_parms() (pygor3.IgorIO.IgorModel_Marginals method) insert_IgorAlignments_FromCSVline() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorBestScenarios_FromCSVline() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorBestScenariosVDJ_FromCSVline() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) insert_IgorEvent_realization_FromDict() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorGeneAnchors_FromCSVline() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorGeneTemplate_FromBioRecord() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorIndexedCDR3_FromCSVline() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorIndexedSeq_FromCSVline() (in module pygor3.IgorIndexedSequencesDB) (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorModel_Marginals_FromDict() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_IgorRec_Event_FromDict() (pygor3.IgorSqliteDB.IgorSqliteDB method) insert_load_IgorPgen_FromCSVline() (pygor3.IgorSqliteDB.IgorSqliteDB method) InsertSegment (class in pygor3.utils)

J

J (pygor3.IgorIO.IgorRefGenome property)

J_anchor() (pygor3.IgorIO.IgorModel method) J_anchors (pygor3.IgorIO.IgorModel property)

L

list_from_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) list_of_fields() (pygor3.AIRR.AIRR_VDJ_rearrangement static method) load() (pygor3.IgorIO.IgorIndexedSequence class method) load_config_files() (in module pygor3.config) load_dataframes() (pygor3.IgorIO.IgorAnchors method) load_dataframes_from_dict() (pygor3.IgorIO.IgorRefGenome method) load_dataframes_from_ref_genome_files() (pygor3.IgorIO.IgorRefGenome method) load_db() (pygor3.IgorIO.IgorTask method) (pygor3.IgorSqliteDB.IgorSqliteDB method) load_db_from_alignments() (pygor3.IgorIO.IgorTask method) load_db_from_anchors() (pygor3.IgorIO.IgorTask method) load_db_from_bestscenarios() (pygor3.IgorIO.IgorTask method) load_db_from_genomes() (pygor3.IgorIO.IgorTask method) load_db_from_indexed_cdr3() (pygor3.IgorIO.IgorTask method) load_db_from_indexed_sequences() (pygor3.IgorIO.IgorTask method) load_db_from_inferred_model() (pygor3.IgorIO.IgorTask method) load_db_from_models() (pygor3.IgorIO.IgorTask method) load_db_from_pgen() (pygor3.IgorIO.IgorTask method) load_default() (pygor3.IgorIO.IgorModel class method) (pygor3.IgorIO.IgorModel_Parms class method) (pygor3.IgorIO.IgorRefGenome class method) load_Deletion_realizations_by_nickname() (pygor3.IgorIO.IgorModel_Parms method) load_DinucMarkov_realizations_by_nickname() (pygor3.IgorIO.IgorModel_Parms method) load_events_from_dict() (pygor3.IgorIO.IgorModel_Parms method) load_from_batchname() (pygor3.IgorIO.IgorTask class method) load_from_dataframe_genomics_dict() (pygor3.IgorIO.IgorRefGenome class method) load_from_dict() (pygor3.IgorIO.IgorScenario class method) load_from_directory() (pygor3.IgorIO.IgorModel class method) load_from_networkx() (pygor3.IgorIO.IgorModel class method) load_from_parms_marginals_object() (pygor3.IgorIO.IgorModel class method) load_from_path() (pygor3.IgorIO.IgorAnchors class method) (pygor3.IgorIO.IgorRefGenome class method) load_from_txt() (pygor3.IgorIO.IgorModel class method) load_FromCSVline() (pygor3.IgorIndexedSequence.IgorIndexedSequence class method) load_FromCSVLine() (pygor3.IgorIO.IgorAlignment_data class method) load_FromCSVline() (pygor3.IgorIO.IgorIndexedSequence class method) load_FromDict() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ class method) (pygor3.IgorIO.IgorBestScenariosVDJ class method) load_FromEventNameValues() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ class method) (pygor3.IgorIO.IgorBestScenariosVDJ class method) load_FromLineBestScenario() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ class method) (pygor3.IgorIO.IgorBestScenariosVDJ class method) (pygor3.IgorIO.IgorScenario class method)

load_FromSQLRecord() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ class method) (pygor3.IgorIndexedSequence.IgorIndexedSequence class method) (pygor3.IgorIO.IgorAlignment_data class method) (pygor3.IgorIO.IgorBestScenariosVDJ class method) (pygor3.IgorIO.IgorIndexedSequence class method) (pygor3.IgorIO.IgorScenario class method) load_FromSQLRecord_list() (pygor3.IgorIO.IgorRefGenome class method) load_GeneChoice_realizations_by_nickname() (pygor3.IgorIO.IgorModel_Parms method) load_genomicDs_from_file() (pygor3.IgorIO.IgorRefGenome method) load_genomicJs_from_file() (pygor3.IgorIO.IgorRefGenome method) load_genomicVs_from_file() (pygor3.IgorIO.IgorRefGenome method) load_IgorAlignments_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorBestScenarios_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorBestScenariosVDJ_FromCSV() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) load_IgorGeneAnchors_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorGeneTemplate_FromFASTA() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorIndexedCDR3_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorIndexedSeq_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorModel() (pygor3.IgorIO.IgorTask method) (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorModel_from_infer_files() (pygor3.IgorIO.IgorTask method) load_IgorModel_FromTXT() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorModel_Marginals() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorModel_Parms() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorPgen_FromCSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_IgorRefGenome() (pygor3.IgorIO.IgorTask method) load_Insertion_realizations_by_nickname() (pygor3.IgorIO.IgorModel_Parms method) load_J_anchors_from_file() (pygor3.IgorIO.IgorRefGenome method) load_J_dataframe() (pygor3.IgorIO.IgorAnchors method) load_mdl_from_db() (pygor3.IgorIO.IgorTask method) load_records_from_fasta() (in module pygor3.imgt) load_V_anchors_from_file() (pygor3.IgorIO.IgorRefGenome method) load_V_dataframe() (pygor3.IgorIO.IgorAnchors method) load_VDJ_BS_database() (pygor3.IgorIO.IgorTask method) load_VDJ_database() (pygor3.IgorIO.IgorTask method) load_VDJ_Database() (pygor3.IgorSqliteDB.IgorSqliteDB method) load_VDJ_from_IMGT_website() (pygor3.IgorIO.IgorRefGenome class method) load_VJ_from_IMGT_website() (pygor3.IgorIO.IgorRefGenome class method) loadDataBase() (pygor3.IgorIndexedSequencesDB.IgorIndexedSequencesDB class method)

M

main() (in module pygor3.scripts.all_gene_alignments_id) (in module pygor3.scripts.bs_export) (in module pygor3.scripts.bs_pairwise_prob) (in module pygor3.scripts.download_imgt_gene_templates) (in module pygor3.scripts.get_imgt_data) (in module pygor3.scripts.infer_sequences) (in module pygor3.scripts.load_database) (in module pygor3.scripts.model_create) (in module pygor3.scripts.model_export) (in module pygor3.scripts.model_plot) (in module pygor3.scripts.naive_align) (in module pygor3.scripts.naive_align_id) (in module pygor3.scripts.observable) (in module pygor3.scripts.pgen_sequences) (in module pygor3.scripts.plot_marginals) (in module pygor3.scripts.scriptTest) (in module pygor3.scripts.scriptTest02) (in module pygor3.scripts.short_names_imgt_templates) (in module pygor3.scripts.stas_from_bs) main_old() (in module pygor3.scripts.observable) make_default_from_Dataframe_dict() (pygor3.IgorIO.IgorModel class method) make_default_model_from_IgorRefGenome() (pygor3.IgorIO.IgorModel class method) make_default_VDJ() (pygor3.IgorIO.IgorModel class method) (pygor3.IgorIO.IgorModel_Parms class method) make_default_VDJ_from_IgorRefGenome() (pygor3.IgorIO.IgorModel_Parms class method) make_default_VJ() (pygor3.IgorIO.IgorModel class method) (pygor3.IgorIO.IgorModel_Parms class method) make_igor_directories() (in module pygor3.utils) make_model_default_VDJ_from_dataframes() (pygor3.IgorIO.IgorModel class method) make_model_default_VDJ_from_fasta_files() (pygor3.IgorIO.IgorTask method) make_model_default_VDJ_from_genomes_dir() (pygor3.IgorIO.IgorTask method) make_model_default_VJ_from_dataframes() (pygor3.IgorIO.IgorModel class method) make_model_default_VJ_from_genomes_dir() (pygor3.IgorIO.IgorTask method) make_uniform_from_parms() (pygor3.IgorIO.IgorModel_Marginals class method) make_VDJ_model() (in module pygor3.imgt)

Model (in module pygor3.IgorIO) module pygor3 pygor3.AIRR pygor3.config pygor3.IgorBestScenarios pygor3.IgorDefaults pygor3.IgorDictionaries pygor3.IgorIndexedSequence pygor3.IgorIndexedSequencesDB pygor3.IgorIO pygor3.IgorSQL pygor3.IgorSqliteDB pygor3.IgorSqliteDBBestScenarios pygor3.imgt pygor3.scripts pygor3.scripts.all_gene_alignments_id pygor3.scripts.bs_export pygor3.scripts.bs_pairwise_prob pygor3.scripts.download_imgt_gene_templates pygor3.scripts.get_imgt_data pygor3.scripts.infer_sequences pygor3.scripts.load_database pygor3.scripts.model_create pygor3.scripts.model_export pygor3.scripts.model_plot pygor3.scripts.naive_align pygor3.scripts.naive_align_id pygor3.scripts.observable pygor3.scripts.pgen_sequences pygor3.scripts.plot_marginals pygor3.scripts.scriptTest pygor3.scripts.scriptTest02 pygor3.scripts.short_names_imgt_templates pygor3.scripts.stas_from_bs pygor3.utils

N

naive_align() (in module pygor3.IgorIO)

name (pygor3.IgorIO.IgorEvent_realization attribute) np_seq_to_str_seq() (in module pygor3.utils)

O

observable() (in module pygor3.scripts.observable)

P

parse_scenarios_to_airr() (pygor3.IgorIO.IgorTask method) Pconditionals (pygor3.IgorIO.IgorModel property) pd_realizations (pygor3.IgorIO.IgorRec_Event property) plot() (pygor3.IgorIO.IgorModel method) plot_Bayes_network() (pygor3.IgorIO.IgorModel method) plot_Event() (pygor3.IgorIO.IgorModel method) plot_event_Deletion() (pygor3.IgorIO.IgorModel method) plot_event_DinucMarkov() (pygor3.IgorIO.IgorModel method) plot_event_GeneChoice() (pygor3.IgorIO.IgorModel method) plot_event_Insertion() (pygor3.IgorIO.IgorModel method) plot_Event_Marginal() (pygor3.IgorIO.IgorModel method) plot_GeneChoice_Pmarginal() (pygor3.IgorIO.IgorModel method) plot_Graph() (pygor3.IgorIO.IgorModel_Parms method) plot_InsertionsDeletions_Pmarginal() (pygor3.IgorIO.IgorModel method) plot_mutual_information() (pygor3.IgorIO.IgorModel static method) plot_np_aln_sequences() (in module pygor3.utils) plot_recombination_entropy() (pygor3.IgorIO.IgorModel method) plot_scenario() (pygor3.IgorIO.IgorModel method) plot_scenario_from_da_scenario_aln() (in module pygor3.utils) pygor3 module pygor3.AIRR module pygor3.config module pygor3.IgorBestScenarios module pygor3.IgorDefaults module pygor3.IgorDictionaries module pygor3.IgorIndexedSequence module pygor3.IgorIndexedSequencesDB module pygor3.IgorIO module pygor3.IgorSQL module pygor3.IgorSqliteDB module pygor3.IgorSqliteDBBestScenarios module

pygor3.imgt module pygor3.scripts module pygor3.scripts.all_gene_alignments_id module pygor3.scripts.bs_export module pygor3.scripts.bs_pairwise_prob module pygor3.scripts.download_imgt_gene_templates module pygor3.scripts.get_imgt_data module pygor3.scripts.infer_sequences module pygor3.scripts.load_database module pygor3.scripts.model_create module pygor3.scripts.model_export module pygor3.scripts.model_plot module pygor3.scripts.naive_align module pygor3.scripts.naive_align_id module pygor3.scripts.observable module pygor3.scripts.pgen_sequences module pygor3.scripts.plot_marginals module pygor3.scripts.scriptTest module pygor3.scripts.scriptTest02 module pygor3.scripts.short_names_imgt_templates module pygor3.scripts.stas_from_bs module pygor3.utils module

Q

Q_align_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_align_in_db_by_gene() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_CDR3_Anchors_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_IgorBestScenarios_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_IgorPgen_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method)

Q_model_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_output_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_ref_genome_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_ref_genome_in_db_by_gene() (pygor3.IgorSqliteDB.IgorSqliteDB method) Q_sequences_in_db() (pygor3.IgorSqliteDB.IgorSqliteDB method)

R

RcParams (class in pygor3.config) read_Edges() (pygor3.IgorIO.IgorModel_Parms method) read_ErrorRate() (pygor3.IgorIO.IgorModel_Parms method) read_Event_list() (pygor3.IgorIO.IgorModel_Parms method) read_model_from_directory() (pygor3.IgorIO.IgorModel method) read_model_from_txt() (pygor3.IgorIO.IgorModel method) read_model_marginals() (pygor3.IgorIO.IgorModel_Marginals method) read_model_parms() (pygor3.IgorIO.IgorModel_Parms method) realiz_dict_from_scenario() (pygor3.IgorIO.IgorModel_Parms method) realization() (pygor3.IgorIO.IgorModel method) realizations_dict() (pygor3.IgorIO.IgorModel method) RefGenome (in module pygor3.IgorIO) remove_Edge() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorModel_Parms method)

run_align() (pygor3.IgorIO.IgorTask method) run_clean_batch() (pygor3.IgorIO.IgorTask method) run_command() (in module pygor3.IgorIO) run_command_no_output() (in module pygor3.IgorIO) run_command_print() (in module pygor3.IgorIO) run_datadir() (pygor3.IgorIO.IgorTask method) run_demo() (pygor3.IgorIO.IgorTask method) run_generate_to_dataframe() (pygor3.IgorIO.IgorTask method) run_get_igor_datadir() (in module pygor3.utils) run_get_igor_exec_path() (in module pygor3.utils) run_get_igor_wd() (in module pygor3.utils) run_get_random_string() (in module pygor3.utils) run_pgen() (pygor3.IgorIO.IgorTask method) run_read_seqs() (pygor3.IgorIO.IgorTask method) run_scenarios() (pygor3.IgorIO.IgorTask method)

S

save_records2fasta() (in module pygor3.imgt) save_scenario_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) save_SONIA_mdl_dirname() (in module pygor3.IgorIO) scenario_from_database() (pygor3.IgorIO.IgorModel method) set_Edges_from_dict() (pygor3.IgorIO.IgorModel_Parms method) set_event_realizations_from_DataFrame() (pygor3.IgorIO.IgorModel_Parms method) set_genomic_dataframe_dict() (pygor3.IgorIO.IgorModel method) set_model() (pygor3.IgorIO.IgorScenario method) set_model_from_headers() (pygor3.IgorIO.IgorScenario method) set_realization_event_from_DataFrame() (pygor3.IgorIO.IgorModel method) set_realization_vector() (pygor3.IgorIO.IgorRec_Event method)

set_realization_vector_GeneChoice() (pygor3.IgorIO.IgorRec_Event method) setAlignsFile() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) setInputSeqsFile() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) setModel() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) setModel_Parms() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) setModelFromFiles() (pygor3.IgorSqliteDBBestScenarios.IgorSqliteDBBestScenariosVDJ method) sqlcmd_ct_BestScenarios() (in module pygor3.IgorSQL) sqlcmd_ct_Model_Marginals() (in module pygor3.IgorSQL) sqlcmd_ct_Model_Marginals_DinucMarkov() (in module pygor3.IgorSQL) str_scenario_fasta() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) str_seq_to_np_seq() (in module pygor3.utils)

T

to_dict() (pygor3.AIRR.AIRR_gene method) (pygor3.AIRR.AIRR_VDJ_rearrangement method) (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIndexedSequence.IgorIndexedSequence method) (pygor3.IgorIO.IgorAlignment_data method) (pygor3.IgorIO.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorEvent_realization method) (pygor3.IgorIO.IgorIndexedSequence method) (pygor3.IgorIO.IgorRec_Event method) (pygor3.IgorIO.IgorRefGenome method) (pygor3.IgorIO.IgorScenario method) (pygor3.IgorIO.IgorTask method)

to_dict_export() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) to_dict_names() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) to_dict_ntsequences() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method) (pygor3.IgorIO.IgorBestScenariosVDJ method) to_dict_values() (pygor3.IgorBestScenarios.IgorBestScenariosVDJ method)

U

ufunc_log_pxy_over_px_py() (in module pygor3.utils) update_batch_filenames() (pygor3.IgorIO.IgorTask method) update_batchname() (pygor3.IgorIO.IgorTask method) update_default_filenames() (pygor3.IgorIO.IgorAnchors method) update_events_name() (pygor3.IgorIO.IgorModel_Parms method) update_fln_names() (pygor3.IgorIO.IgorRefGenome method) update_igor_batch_dict() (in module pygor3.IgorDictionaries)

update_model_filenames() (pygor3.IgorIO.IgorTask method) update_name() (pygor3.IgorIO.IgorRec_Event method) update_network_dict_from_model_parms() (pygor3.IgorIO.IgorModel_Marginals method) update_pd_realizations_from_realizations() (pygor3.IgorIO.IgorRec_Event method) update_realizations_from_dataframe() (pygor3.IgorIO.IgorRec_Event method) update_realizations_from_fasta() (pygor3.IgorIO.IgorRec_Event method) update_ref_genome() (pygor3.IgorIO.IgorTask method)

V

V (pygor3.IgorIO.IgorRefGenome property) V_anchor() (pygor3.IgorIO.IgorModel method) V_anchors (pygor3.IgorIO.IgorModel property) value (pygor3.IgorIO.IgorEvent_realization attribute)

VE_get_factors_by_sum_out_variable() (pygor3.IgorIO.IgorModel method) VE_get_Pmarginal_of_event() (pygor3.IgorIO.IgorModel method) VE_get_Pmarginals_initial_factors() (pygor3.IgorIO.IgorModel method) view_alignment() (in module pygor3.utils)

W

w_average_function_df_scenarios() (pygor3.IgorIO.IgorModel method) w_covariance_df_scenarios() (pygor3.IgorIO.IgorModel method) w_mean_df_scenarios() (pygor3.IgorIO.IgorModel method) w_variance_df_scenarios() (pygor3.IgorIO.IgorModel method) write_df_scenario_aln_FASTA() (pygor3.IgorIO.IgorModel method) write_Edges() (pygor3.IgorIO.IgorModel_Parms method) write_ErrorRate() (pygor3.IgorIO.IgorModel_Parms method) write_Event_list() (pygor3.IgorIO.IgorModel_Parms method) write_event_probabilities() (pygor3.IgorIO.IgorModel_Marginals method) write_geneanchors_dataframe_to_csv() (in module pygor3.utils) write_genetemplate_dataframe_to_fasta() (in module pygor3.utils) write_IgorAlignments2Fasta() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorAlignments_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorBestScenarios_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorGeneAnchors_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorGeneTemplate_to_fasta() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorIndexedCDR3_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method)

write_IgorIndexedSeq_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorModel_Marginals_to_TXT() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorModel_Parms_to_TXT() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorModel_to_TXT() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_IgorPgen_to_CSV() (pygor3.IgorSqliteDB.IgorSqliteDB method) write_mdldata_dir() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorTask method) write_model() (pygor3.IgorIO.IgorModel method) write_model_marginals() (pygor3.IgorIO.IgorModel_Marginals method) write_model_parms() (pygor3.IgorIO.IgorModel_Parms method) write_ref_genome() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorRefGenome method) write_ref_genome_dir() (pygor3.IgorIO.IgorModel method) (pygor3.IgorIO.IgorModel_Parms method) (pygor3.IgorIO.IgorRefGenome method) write_ref_genome_files_from_dataframe() (in module pygor3.utils) write_sequences_to_file() (in module pygor3.utils)