Table of Contents - full_lengther_next-1.0.1 Documentation
Classes and Modules
- Cdhit
- ChimericSeqs
- CommonFunctions
- ExoBlastHit
- ExonerateResult
- FlAnalysis
- FlnStats
- FullLengtherNext
- Mapping
- Mpileup
- MyWorker
- MyWorkerEst
- MyWorkerManagerEst
- MyWorkerManagerFln
- NcRna
- Object
- Orf
- ScbiMapreduce
- ScbiMapreduce::WorkManager
- Seq
- Sequence
- String
- TestCode
- UneLosHit
Methods
- ::asign_coding_attributes — MyWorkerManagerFln
- ::correct_by_selected — MyWorkerManagerFln
- ::end_work_manager — MyWorkerManagerEst
- ::end_work_manager — MyWorkerManagerFln
- ::get_annotations — MyWorkerManagerFln
- ::get_array_seqs — MyWorkerManagerEst
- ::get_coding_info — MyWorkerManagerFln
- ::get_max_score — MyWorkerManagerFln
- ::get_min_Xratio — MyWorkerManagerFln
- ::get_scores — MyWorkerManagerFln
- ::get_seqs — MyWorkerManagerFln
- ::init_work_manager — MyWorkerManagerEst
- ::init_work_manager — MyWorkerManagerFln
- ::load_functional_annotations — MyWorkerManagerFln
- ::new — Seq
- ::new — Cdhit
- ::new — ExoBlastHit
- ::new — ExonerateResult
- ::new — Mpileup
- ::new — Mapping
- ::new — Orf
- ::new — Sequence
- ::new — TestCode
- ::new — UneLosHit
- ::orf_prediction_with_transdecoder — MyWorkerManagerFln
- ::repTrans_keep_seq — MyWorkerManagerFln
- ::select_orf — MyWorkerManagerFln
- #add_orf — Sequence
- #add_percentages_by_scalar — FlnStats
- #add_percentages_by_vector — FlnStats
- #add_region — TestCode
- #ajust_nt — UneLosHit
- #all_warns — Sequence
- #analiza_orf_y_fl — FlAnalysis
- #analysis_over_DB_annotated_seqs — Object
- #area_without_annotation? — Sequence
- #artifact? — Object
- #blastEST — MyWorkerEst
- #blast_analysis — MyWorkerEst
- #calcParam — TestCode
- #calculate_coverage_parameters — Mapping
- #calculate_n50_n90 — FlnStats
- #calification — Sequence
- #cd_hit_clusters — Cdhit
- #change_degenerated_nt! — Sequence
- #check_blast — MyWorker
- #check_frame_shift — CommonFunctions
- #check_mapping — MyWorker
- #check_ncRNA — MyWorker
- #check_prot_db — MyWorker
- #check_testcode — MyWorker
- #check_warn — Sequence
- #clean_annotations — Sequence
- #clean_by_identity — Object
- #clean_by_query_length_match — Object
- #clean_hsp_by_identity — Object
- #clean_orfs — Sequence
- #clean_overlapping_hsps — Object
- #clean_subjec_ids_name — MyWorker
- #clean_subject_overlapping_hsps — Object
- #clean_warnings — Sequence
- #clone — Sequence
- #clone_annotations — Sequence
- #clone_warnings — Sequence
- #close — Mpileup
- #closing_worker — MyWorker
- #cluster_hsps — Object
- #cluster_query_hits — ChimericSeqs
- #clustering_by_annot — Object
- #clustering_by_id — Object
- #coding_stats_reptrans — FlnStats
- #compare_regions — TestCode
- #compare_regions_old — TestCode
- #compare_seq_length_with_subject — FlAnalysis
- #complementary_dna — String
- #confirm_chimeras — ChimericSeqs
- #contenidos_en_prot — CommonFunctions
- #convert_parsed_lines — ExonerateResult
- #corrige_frame — CommonFunctions
- #countBases — TestCode
- #count_cpu — Object
- #define_hit_limits — ChimericSeqs
- #define_hit_parameters — ExonerateResult
- #define_homology_zones — ChimericSeqs
- #delete_zones — ChimericSeqs
- #determine_status — FlAnalysis
- #do_blast_with_EST — Object
- #do_clustal — ChimericSeqs
- #do_makeblastdb — Object
- #do_map — Mapping
- #do_ref — Mapping
- #do_reverso_complementary — ExonerateResult
- #do_samtools_ref — Mapping
- #duplicate_hits — ChimericSeqs
- #each_cluster — Cdhit
- #empty? — ExonerateResult
- #error_received — MyWorkerManagerEst
- #error_received — MyWorkerManagerFln
- #exonerate_fix_frame_shift — FlAnalysis
- #extend_match — CommonFunctions
- #filter_hits — Object
- #find_end — FlAnalysis
- #find_hit — Object
- #find_nc_rna — NcRna
- #find_query — ExonerateResult
- #find_start — FlAnalysis
- #fix_degenerated_fasta! — Sequence
- #format_chimera! — Sequence
- #fragment_chimera — ChimericSeqs
- #full_lenghter2 — MyWorker
- #generate_orf_old — String
- #generate_uncomplete_orf — TestCode
- #getConclusion — TestCode
- #get_acc — Sequence
- #get_all_master — Cdhit
- #get_coverage_parameters — Mapping
- #get_coverage_subject — Object
- #get_fasta — Sequence
- #get_functional_annotations — MyWorkerManagerFln
- #get_hits — ChimericSeqs
- #get_limits — ChimericSeqs
- #get_limits_s — ChimericSeqs
- #get_master — Cdhit
- #get_pident — Sequence
- #get_prot_sequences — MyWorker
- #get_sp — Cdhit
- #get_taxonomy — FlnStats
- #go_for_graph — Object
- #handle_data_main_summary — FlnStats
- #handle_data_reptrans_summary — FlnStats
- #hash_fasta — Cdhit
- #hit_is_in? — ChimericSeqs
- #hit_move_limits — ChimericSeqs
- #hit_set_q_len — ChimericSeqs
- #hiting — ExonerateResult
- #hits_misma_id — UneLosHit
- #hits_statistics — MyWorker
- #hsps_relationship_subject — Object
- #idxstats — Mapping
- #index — Mapping
- #initialize_contig — Mpileup
- #initialize_stats_hash — FlnStats
- #initialize_stats_hash_reptrans — FlnStats
- #inspect — ExonerateResult
- #last_stats — FlnStats
- #load_cd_hit_sequences_names — Object
- #load_isoform_hash — Object
- #load_seq_in_hash — Object
- #map_transcriptome — MyWorker
- #mark_nt_seqs — FlAnalysis
- #master_fasta — Cdhit
- #master_to_sp_seq — Cdhit
- #match_with_gapped_reference — CommonFunctions
- #match_with_ungapped_reference — CommonFunctions
- #min_distance_between_homology_zones — ChimericSeqs
- #misassembled_detection — Object
- #modify_3p_align — FlAnalysis
- #modify_5p_align — FlAnalysis
- #move_limits — ChimericSeqs
- #mpileup — Mapping
- #multiple_hsps — Object
- #next_work — MyWorkerManagerEst
- #next_work — MyWorkerManagerFln
- #orf_finder_old — String
- #orf_fusion — TestCode
- #overlapped_hits — UneLosHit
- #overlapped_hits_query — UneLosHit
- #overlapping_hits? — UneLosHit
- #overlapping_hsps_on_subject — Object
- #overlapping_zones — ChimericSeqs
- #overlaps? — Orf
- #parse_db — Seq
- #parse_file — ExonerateResult
- #parse_idxstats — Mapping
- #parse_member — Cdhit
- #parse_mpileup — Mapping
- #print_alignment — Sequence
- #process_object — MyWorker
- #process_object — MyWorkerEst
- #prot_annot_calification — Sequence
- #read_contig — Mpileup
- #receive_fln_data — MyWorkerManagerFln
- #receive_initial_config — MyWorker
- #receive_initial_config — MyWorkerEst
- #receive_mapping_data — MyWorkerManagerFln
- #recover_different_lengths — Cdhit
- #reduce_coordinates — Sequence
- #reduce_pool_sequences — Object
- #refine_analysis_with_exonerate — MyWorker
- #refine_match — CommonFunctions
- #repTrans_keep_seq — MyWorkerManagerFln
- #replace_hits — MyWorker
- #report — Mapping
- #report_clustering — Object
- #reptrans — Object
- #rescue_sequence — MyWorker
- #reset_classification — Sequence
- #reverse_seq — CommonFunctions
- #run_blast — MyWorker
- #same_frame_hits — UneLosHit
- #same_frame_hits_query — UneLosHit
- #same_query_hsp — Object
- #same_sense? — Object
- #same_subject_hsp — Object
- #save_annotations — FlAnalysis
- #scan_sequences — CommonFunctions
- #search_best_orf_y_fl — MyWorker
- #search_chimeras — ChimericSeqs
- #search_ident_prots — ChimericSeqs
- #select_hits_by_coverage_subject — Object
- #select_hits_by_evalue — Object
- #select_hits_by_identity_query — Object
- #select_hsps_by_id — Object
- #select_representative — Object
- #select_seqs_more_500pb — Object
- #select_seqs_with_name — Object
- #select_sequences — MyWorker
- #send_fln_data — MyWorkerManagerFln
- #send_mapping_data — MyWorkerManagerFln
- #send_next_work — ScbiMapreduce::WorkManager
- #separated_hits — UneLosHit
- #separated_hits? — UneLosHit
- #separated_hits_query — UneLosHit
- #sequence_stats — FlnStats
- #set_cut_positions — ChimericSeqs
- #set_ident — ExonerateResult
- #set_limits — ChimericSeqs
- #set_start_codon — FlAnalysis
- #set_thresold_evalue — Object
- #show_alignment — Sequence
- #show_nts — FlAnalysis
- #size — ExonerateResult
- #subject_overlapping_hsps — Object
- #summary_stats — FlnStats
- #t_code — TestCode
- #t_code_old — TestCode
- #table_title — FlnStats
- #testCode_exec — TestCode
- #test_code — Sequence
- #to_s — Seq
- #too_many_errors_received — MyWorkerManagerEst
- #too_many_errors_received — MyWorkerManagerFln
- #transdecoder_keep_seq — MyWorkerManagerFln
- #translate — String
- #type_fusion — TestCode
- #uncomplete_orf_finder — TestCode
- #unmapped? — Sequence
- #useContParam — TestCode
- #usePosParam — TestCode
- #warnings — Sequence
- #window_walking — TestCode
- #work_received — MyWorkerManagerEst
- #work_received — MyWorkerManagerFln
- #worker_initial_config — MyWorkerManagerEst
- #worker_initial_config — MyWorkerManagerFln
- #write_align — Sequence
- #write_chimera — Sequence
- #write_coding — Sequence
- #write_fasta — Object
- #write_info — Sequence
- #write_mapping_report — FlnStats
- #write_misassembled — Sequence
- #write_ncrna — Sequence
- #write_nt_seq — Sequence
- #write_other — Sequence
- #write_prot_annot — Sequence
- #write_prot_seq — Sequence
- #write_querys — MyWorker
- #write_reptrans_stats — FlnStats
- #write_seq — MyWorkerManagerFln
- #write_summary_stats — FlnStats
- #write_targets — MyWorker
- #write_txt — FlnStats
- #write_unknown — Sequence
- #write_unmapped — Sequence