Method List
Search:
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#add_orf Sequence
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#add_percentages_by_scalar FlnStats
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#add_percentages_by_vector FlnStats
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#add_region TestCode
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#ajust_nt UneLosHit
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#all_warns Sequence
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#analiza_orf_y_fl FlAnalysis
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#analysis_over_DB_annotated_seqs Top Level Namespace
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#area_without_annotation Sequence
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#area_without_annotation? Sequence
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#artifact? Top Level Namespace
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asign_coding_attributes MyWorkerManagerFln
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#blastEST MyWorkerEst
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#blast_analysis MyWorkerEst
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#calcParam TestCode
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#calculate_n50_n90 FlnStats
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#calification Sequence
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#cd_hit_clusters Cdhit
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#change_degenerated_nt! Sequence
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#check_blast MyWorker
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#check_frame_shift CommonFunctions
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#check_mapping MyWorker
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#check_ncRNA MyWorker
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#check_prot_db MyWorker
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#check_testcode MyWorker
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#check_warn Sequence
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#clean_annotations Sequence
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#clean_by_identity Top Level Namespace
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#clean_by_query_length_match Top Level Namespace
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#clean_hsp_by_identity Top Level Namespace
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#clean_orfs Sequence
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#clean_overlapping_hsps Top Level Namespace
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#clean_subjec_ids_name MyWorker
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#clean_subject_overlapping_hsps Top Level Namespace
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#clean_warnings Sequence
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#clone Sequence
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#clone_annotations Sequence
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#clone_warnings Sequence
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#close Mpileup
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#closing_worker MyWorker
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#cluster_hsps Top Level Namespace
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#cluster_query_hits ChimericSeqs
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#clustering_by_annot Top Level Namespace
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#clustering_by_id Top Level Namespace
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#clusters Cdhit
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#coding_stats_reptrans FlnStats
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#comments Seq
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#compare_regions TestCode
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#compare_regions_old TestCode
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#compare_seq_length_with_subject FlAnalysis
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#complementary_dna String
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#confirm_chimeras ChimericSeqs
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#contenidos_en_prot CommonFunctions
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#convert_parsed_lines ExonerateResult
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correct_by_selected MyWorkerManagerFln
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#corrige_frame CommonFunctions
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#countBases TestCode
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#count_cpu Top Level Namespace
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#coverage_analysis Sequence
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#db Seq
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#db Sequence
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#db_name Sequence
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#define_hit_limits ChimericSeqs
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#define_hit_parameters ExonerateResult
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#define_homology_zones ChimericSeqs
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#delete_zones ChimericSeqs
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#determine_status FlAnalysis
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#do_blast_with_EST Top Level Namespace
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#do_clustal ChimericSeqs
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#do_makeblastdb Top Level Namespace
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#do_map Mapping
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#do_ref Mapping
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#do_reverso_complementary ExonerateResult
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#do_samtools_ref Mapping
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#duplicate_hits ChimericSeqs
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#each_cluster Cdhit
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#empty? ExonerateResult
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end_work_manager MyWorkerManagerEst
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end_work_manager MyWorkerManagerFln
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#error_received MyWorkerManagerFln
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#error_received MyWorkerManagerEst
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#exonerate_fix_frame_shift FlAnalysis
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#extend_match CommonFunctions
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#fasta_length Sequence
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#filter_hits Top Level Namespace
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#final_hit UneLosHit
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#find_end FlAnalysis
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#find_hit Top Level Namespace
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#find_nc_rna NcRna
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#find_query ExonerateResult
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#find_start FlAnalysis
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#fix_degenerated_fasta! Sequence
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#format_chimera! Sequence
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#fpkm Sequence
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#fragment_chimera ChimericSeqs
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#frame Orf
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#ft Bio::UniProtKB
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#full_lenghter2 MyWorker
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#full_prot UneLosHit
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#functional_annotations Sequence
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#generate_orf_old String
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#generate_uncomplete_orf TestCode
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#getConclusion TestCode
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#get_acc Sequence
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#get_all_master Cdhit
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get_annotations MyWorkerManagerFln
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get_array_seqs MyWorkerManagerEst
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get_coding_info MyWorkerManagerFln
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#get_coverage_subject Top Level Namespace
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#get_fasta Sequence
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#get_functional_annotations MyWorkerManagerFln
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#get_hits ChimericSeqs
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#get_limits ChimericSeqs
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#get_limits_s ChimericSeqs
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#get_master Cdhit
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get_max_score MyWorkerManagerFln
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get_min_Xratio MyWorkerManagerFln
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#get_pident Sequence
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#get_prot_sequences MyWorker
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get_scores MyWorkerManagerFln
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get_seqs MyWorkerManagerFln
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#get_sp Cdhit
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#get_taxonomy FlnStats
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#go_for_graph Top Level Namespace
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#handle_data_main_summary FlnStats
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#handle_data_reptrans_summary FlnStats
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#hash_fasta Cdhit
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#hit Sequence
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#hit_is_in? ChimericSeqs
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#hit_move_limits ChimericSeqs
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#hit_set_q_len ChimericSeqs
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#hiting ExonerateResult
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#hits_misma_id UneLosHit
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#hits_statistics MyWorker
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#hsps_relationship_subject Top Level Namespace
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#id Sequence
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#idxstats Mapping
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#ignore Sequence
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#index Mapping
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init_work_manager MyWorkerManagerFln
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init_work_manager MyWorkerManagerEst
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#initialize Sequence
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#initialize ExonerateResult
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#initialize TestCode
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#initialize Mapping
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#initialize UneLosHit
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#initialize Mpileup
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#initialize Cdhit
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#initialize Seq
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#initialize Orf
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#initialize ExoBlastHit
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#initialize_contig Mpileup
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#initialize_stats_hash FlnStats
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#initialize_stats_hash_reptrans FlnStats
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#inspect ExonerateResult
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#is_ok UneLosHit
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#last_stats FlnStats
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#load_cd_hit_sequences_names Top Level Namespace
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load_functional_annotations MyWorkerManagerFln
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#load_isoform_hash Top Level Namespace
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#load_seq_in_hash Top Level Namespace
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#map_transcriptome MyWorker
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#mark_nt_seqs FlAnalysis
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#master Seq
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#master_fasta Cdhit
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#master_to_sp_seq Cdhit
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#match_with_gapped_reference CommonFunctions
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#match_with_ungapped_reference CommonFunctions
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#min_distance_between_homology_zones ChimericSeqs
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#misassembled_detection Top Level Namespace
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#modify_3p_align FlAnalysis
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#modify_5p_align FlAnalysis
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#move_limits ChimericSeqs
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#mpileup Mapping
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#msgs UneLosHit
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#multiple_hsps Top Level Namespace
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#name Seq
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#next_work MyWorkerManagerFln
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#next_work MyWorkerManagerEst
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#number_x UneLosHit
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#orf_finder_old String
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#orf_fusion TestCode
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orf_prediction_with_transdecoder MyWorkerManagerFln
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#orfs Sequence
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#output_seq UneLosHit
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#overlapped_hits UneLosHit
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#overlapped_hits_query UneLosHit
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#overlapping_hits? UneLosHit
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#overlapping_hsps_on_subject Top Level Namespace
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#overlapping_zones ChimericSeqs
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#overlaps? Orf
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#parse_db Seq
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#parse_file ExonerateResult
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#parse_idxstats Mapping
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#parse_member Cdhit
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#parse_mpileup Mapping
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patched? Bio::UniProtKB
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#print_alignment Sequence
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#process_object MyWorker
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#process_object MyWorkerEst
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#prot_annot_calification Sequence
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#q_frameshift ExoBlastHit
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#q_index_start UneLosHit
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#querys ExonerateResult
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#read_contig Mpileup
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#receive_fln_data MyWorkerManagerFln
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#receive_initial_config MyWorker
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#receive_initial_config MyWorkerEst
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#receive_mapping_data MyWorkerManagerFln
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#reduce_coordinates Sequence
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#reduce_pool_sequences Top Level Namespace
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#refine_analysis_with_exonerate MyWorker
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#refine_match CommonFunctions
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repTrans_keep_seq MyWorkerManagerFln
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#repTrans_keep_seq MyWorkerManagerFln
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#replace_hits MyWorker
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#report Mapping
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#report_clustering Top Level Namespace
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#reptrans Top Level Namespace
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#rescue_sequence MyWorker
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#reset_classification Sequence
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#reverse_seq CommonFunctions
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#run_blast MyWorker
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#s_frameshift ExoBlastHit
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#same_frame_hits UneLosHit
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#same_frame_hits_query UneLosHit
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#same_query_hsp Top Level Namespace
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#same_sense? Top Level Namespace
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#same_subject_hsp Top Level Namespace
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#save_annotations FlAnalysis
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#save_fasta Sequence
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#scan_sequences CommonFunctions
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#score Orf
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#search_best_orf_y_fl MyWorker
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#search_chimeras ChimericSeqs
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#search_ident_prots ChimericSeqs
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#select_hits_by_coverage_subject Top Level Namespace
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#select_hits_by_evalue Top Level Namespace
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#select_hits_by_identity_query Top Level Namespace
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#select_hsps_by_id Top Level Namespace
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select_orf MyWorkerManagerFln
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#select_representative Top Level Namespace
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#select_seqs_more_500pb Top Level Namespace
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#select_seqs_with_name Top Level Namespace
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#select_sequences MyWorker
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#send_fln_data MyWorkerManagerFln
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#send_mapping_data MyWorkerManagerFln
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#send_next_work ScbiMapreduce::WorkManager
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#separated_hits UneLosHit
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#separated_hits? UneLosHit
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#separated_hits_query UneLosHit
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#seq Orf
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#seq_aa Sequence
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#seq_fasta Sequence
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#seq_fasta Seq
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#seq_name Sequence
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#seq_nt Sequence
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#seqs_annotation_prot MyWorkerManagerFln
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#seqs_some_coding MyWorkerManagerFln
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#seqs_unknown MyWorkerManagerFln
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#sequence_hash_fasta Cdhit
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#sequence_stats FlnStats
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#set_cut_positions ChimericSeqs
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#set_ident ExonerateResult
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#set_limits ChimericSeqs
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#set_start_codon FlAnalysis
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#set_thresold_evalue Top Level Namespace
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#show_alignment Sequence
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#show_nts FlAnalysis
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#size ExonerateResult
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#status Sequence
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#status Orf
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#stop_codon Orf
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#subject_overlapping_hsps Top Level Namespace
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#summary_stats FlnStats
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#t_code TestCode
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#t_code Sequence
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#t_code_old TestCode
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#t_end Orf
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#t_start Orf
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#table_title FlnStats
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#testCode_exec TestCode
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#test_code Sequence
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#to_s Seq
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#too_many_errors_received MyWorkerManagerEst
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#too_many_errors_received MyWorkerManagerFln
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#transdecoder_keep_seq MyWorkerManagerFln
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#translate String
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#type Sequence
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#type Orf
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#type_fusion TestCode
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#uncomplete_orf_finder TestCode
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#unmapped? Sequence
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#useContParam TestCode
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#usePosParam TestCode
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#warnings Sequence
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#window_walking TestCode
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#work_received MyWorkerManagerEst
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#work_received MyWorkerManagerFln
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#worker_initial_config MyWorkerManagerEst
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#worker_initial_config MyWorkerManagerFln
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#write_align Sequence
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#write_chimera Sequence
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#write_coding Sequence
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#write_fasta Top Level Namespace
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#write_info Sequence
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#write_mapping_report FlnStats
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#write_misassembled Sequence
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#write_ncrna Sequence
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#write_nt_seq Sequence
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#write_other Sequence
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#write_prot_annot Sequence
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#write_prot_seq Sequence
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#write_querys MyWorker
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#write_reptrans_stats FlnStats
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#write_seq MyWorkerManagerFln
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#write_summary_stats FlnStats
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#write_targets MyWorker
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#write_txt FlnStats
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#write_unknown Sequence
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#write_unmapped Sequence