Table of Contents - gene_assembler-0.0.9 Documentation
Classes and Modules
- BlastTypeParser
- Contig
- Dataset
- ExoBlastQuery
- ExonerateResult
- Feature
- GO
- GeneAssembler
- GffContig
- GffFrameshift
- GffGo
- GffHit
- GffHsp
- GffSNP
- GffStop
- Gff_dataset
- Gff_parser
- Hit
- Hsp
- Localization
- Master_feature
- Object
- Parser
- ParserBlast
- ParserExonerate
- Rebuild
- Report
- ReportGff
- SNP
Methods
- ::new — BlastTypeParser
- ::new — Contig
- ::new — Dataset
- ::new — ExoBlastQuery
- ::new — ExonerateResult
- ::new — Gff_dataset
- ::new — Feature
- ::new — Gff_parser
- ::new — GO
- ::new — Hit
- ::new — Hsp
- ::new — Parser
- ::new — Rebuild
- ::new — Report
- ::new — SNP
- #add_attribs — Feature
- #add_child — Feature
- #add_contig — Dataset
- #add_feature — Gff_dataset
- #add_go — Contig
- #add_hit — Contig
- #add_hsp — Hit
- #add_localization — Contig
- #add_master_feature — Gff_dataset
- #add_parent_to — Gff_dataset
- #add_snp — Contig
- #add_uni_hsp — Rebuild
- #align_contigs — Dataset
- #array_contigs_to_contig — Rebuild
- #attrib — Feature
- #attrib_recover — Dataset
- #build_gene_array — Rebuild
- #cds — Feature
- #change_to_type_id_recursive — Feature
- #clear_clusters — Dataset
- #clr_contigs — Dataset
- #cluster_count — Dataset
- #cluster_filter — Object
- #clustering — Dataset
- #clusters_empty? — Dataset
- #compare — Contig
- #compare — Feature
- #compare — Hsp
- #compare_q — Hsp
- #contig_compact — Rebuild
- #contig_count — Dataset
- #contigs_seq_merge — Rebuild
- #convert_parsed_lines — ExonerateResult
- #coor_intrones — Contig
- #coord_prot — Object
- #correct_hsp_contigs — Dataset
- #correct_hsps — Contig
- #correct_hsps — Hit
- #correct_left_side_contigs — Dataset
- #correct_model — Rebuild
- #count — Feature
- #create — Report
- #create — ReportGff
- #create_dataset — Parser
- #delete_cluster — Dataset
- #delete_cluster_at — Dataset
- #draw — Contig
- #drop_hsp — Hit
- #each_child — Feature
- #each_cluster — Dataset
- #each_cluster_with_index — Dataset
- #each_contig — Dataset
- #each_contig_with_index — Dataset
- #each_feature — Gff_dataset
- #each_go — Contig
- #each_hit — Contig
- #each_hit_with_index — Contig
- #each_hsp — Hit
- #each_hsp_with_index — Hit
- #each_id_feat — Gff_dataset
- #each_id_master — Gff_dataset
- #each_localization — Contig
- #each_localization_with_index — Contig
- #each_master_feature — Gff_dataset
- #each_q_frameshift — Contig
- #each_snp — Contig
- #each_snp_with_index — Contig
- #each_stop — Contig
- #each_stop_with_index — Contig
- #each_tag_attrib — Feature
- #empty? — ExonerateResult
- #eval_model — Rebuild
- #exon_acumulative — Contig
- #exones_q — Contig
- #exones_s — Contig
- #fasta — Dataset
- #fasta_hash — Object
- #feature — Gff_dataset
- #filtering — Dataset
- #filtering_clust — Dataset
- #find_query — ExonerateResult
- #first_hit — Contig
- #first_hsp — Hit
- #format_model — Rebuild
- #frameshift_modified_coordenates — Contig
- #gene_array_and_compact — Rebuild
- #gene_array_report — Rebuild
- #gene_compact — Rebuild
- #gene_error — Rebuild
- #gene_model_cut — Rebuild
- #gene_stadistics — Rebuild
- #gene_stadistics_report — Rebuild
- #generate_file_5_prime — Dataset
- #get — Gff_dataset
- #gff — Contig
- #gff_prot — Contig
- #has_hit? — Contig
- #has_source? — Gff_dataset
- #has_type? — Gff_dataset
- #hit_count — Contig
- #hiting — ExonerateResult
- #hits_sort! — Contig
- #hsp_at — Contig
- #hsp_at — Hit
- #hsp_count — Hit
- #hsp_minor_than? — Contig
- #hsp_minor_than? — Hit
- #hsp_overlap — Hit
- #hsps_correlative? — Hit
- #hsps_sort! — Hit
- #html_footer — Object
- #html_header — Object
- #html_link — Object
- #html_row — Object
- #html_table_footer — Object
- #html_table_header — Object
- #indices — Contig
- #info_clusters — Dataset
- #inspect — ExonerateResult
- #inspects — Gff_dataset
- #inspects — Feature
- #intrones_q — Contig
- #is_gapped? — Contig
- #is_one_hsp? — Contig
- #is_source? — Feature
- #is_truncated? — Contig
- #is_type? — Feature
- #iterative_modeling_gene_w_reference — Rebuild
- #last_hit — Contig
- #last_hsp — Hit
- #length — Feature
- #length2D — Object
- #length= — Contig
- #length_q — Hsp
- #load_dataset — BlastTypeParser
- #load_dataset — Parser
- #load_references — Dataset
- #load_seq — Dataset
- #mapping — Object
- #missing_cluster_transfer — Dataset
- #missing_contigs_transfer — Dataset
- #mixed? — Contig
- #modeling_gene — Rebuild
- #modified_coordenates — Contig
- #modified_coordenates — Hit
- #modified_coordenates — Hsp
- #multiple_align_contigs — Dataset
- #n_contigs? — Dataset
- #n_hits? — Contig
- #n_intron — Contig
- #overlap — Contig
- #overlap_test — Rebuild
- #overlap_with — Hit
- #overlap_with — Hsp
- #parse_attribs — Gff_parser
- #parse_contig_index — Object
- #parse_file — ExonerateResult
- #parse_file — Parser
- #parse_file — ParserBlast
- #parse_file — ParserExonerate
- #parse_stops — Dataset
- #populate_extra_atributes — BlastTypeParser
- #populate_extra_atributes — ParserExonerate
- #position_reference_guided — Rebuild
- #rebuild — Rebuild
- #recover_test — Rebuild
- #report — GffContig
- #report — GffFrameshift
- #report — GffGo
- #report — GffHit
- #report — GffHsp
- #report — Localization
- #report — GffSNP
- #report — GffStop
- #rev — Hsp
- #rev_comp — Contig
- #rev_comp — Dataset
- #rev_comp_if_hit — Contig
- #rev_coord — Contig
- #rev_coord — Hit
- #rev_coord — Hsp
- #score_correction — Dataset
- #sides_add — Object
- #sides_recovery — Object
- #size — ExonerateResult
- #sort_cluster — Dataset
- #sort_cont_clust — Dataset
- #start_codon_search — Contig
- #stop_codon — Contig
- #stop_codon_search — Contig
- #stop_modified_coordenates — Contig
- #transfer_child — Feature
- #transfer_cluster — Dataset
- #transfer_contig_hits — Contig
- #transfer_contig_to_cluster — Dataset
- #transfer_contigs — Dataset
- #transfer_hit — Contig
- #transfer_n_contigs_def_hit_type — Dataset
- #tree — Gff_dataset
- #tree — Feature
- #void_contig — Rebuild
- #web_body — Rebuild
- #web_header — Rebuild
- #within? — Hsp
- #write — Feature
- #write_gbrowse_gff — Rebuild
- #write_model_fasta — Rebuild