Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V _ __init__() (fusor.fusor.FUSOR method) (fusor.harvester.CIVICHarvester method) (fusor.harvester.FusionCallerHarvester method) (fusor.harvester.FusionCallerRecord method) (fusor.harvester.MOAHarvester method) (fusor.translator.Translator method) A AbstractFusion (class in fusor.models) AbstractTranscriptStructuralVariant (class in fusor.models) AdditionalFields (class in fusor.models) ANCHORED_READS (fusor.models.FUSORTypes attribute) AnchoredReads (class in fusor.models) anchoredReads (fusor.models.TranscriptSegmentElement attribute) annot (fusor.fusion_caller_models.Genie attribute) annotated (fusor.harvester.FusionCallerRecord attribute) annotation_error (fusor.harvester.FusionCallerRecord attribute) annots (fusor.fusion_caller_models.STARFusion attribute) Arriba (class in fusor.fusion_caller_models) ARRIBA (fusor.fusion_caller_models.Caller attribute) ArribaHarvester (class in fusor.harvester) ArribaTranslator (class in fusor.translator) Assay (class in fusor.models) assay (fusor.models.AssayedFusion attribute) (fusor.models.InternalTandemDuplication attribute) ASSAYED_FUSION (fusor.models.FusionType attribute) (fusor.models.FUSORTypes attribute) assayed_fusion() (fusor.fusor.FUSOR static method) AssayedFusion (class in fusor.models) assayId (fusor.models.Assay attribute) assayName (fusor.models.Assay attribute) associatedGene (fusor.models.FunctionalDomain attribute) (fusor.models.RegulatoryElement attribute) ATTENUATOR (fusor.models.RegulatoryClass attribute) B base1 (fusor.fusion_caller_models.JAFFA attribute) base2 (fusor.fusion_caller_models.JAFFA attribute) BaseModelForbidExtra (class in fusor.models) BaseStructuralElement (class in fusor.models) break_3prime (fusor.fusion_caller_models.EnFusion attribute) break_5prime (fusor.fusion_caller_models.EnFusion attribute) breakpoint1 (fusor.fusion_caller_models.Arriba attribute) breakpoint2 (fusor.fusion_caller_models.Arriba attribute) BREAKPOINT_COVERAGE (fusor.models.FUSORTypes attribute) BreakpointCoverage (class in fusor.models) C CAAT_SIGNAL (fusor.models.RegulatoryClass attribute) Caller (class in fusor.fusion_caller_models) CATEGORICAL_FUSION (fusor.models.FusionType attribute) (fusor.models.FUSORTypes attribute) categorical_fusion() (fusor.fusor.FUSOR static method) CategoricalFusion (class in fusor.models) CAUSATIVE_EVENT (fusor.models.FUSORTypes attribute) CausativeEvent (class in fusor.models) causativeEvent (fusor.models.AssayedFusion attribute) (fusor.models.InternalTandemDuplication attribute) check_data_resources() (in module fusor.tools) check_exons() (fusor.models.TranscriptSegmentElement method) chr_3prime (fusor.fusion_caller_models.Cicero attribute) (fusor.fusion_caller_models.EnFusion attribute) chr_5prime (fusor.fusion_caller_models.Cicero attribute) (fusor.fusion_caller_models.EnFusion attribute) chrom1 (fusor.fusion_caller_models.JAFFA attribute) chrom2 (fusor.fusion_caller_models.JAFFA attribute) Cicero (class in fusor.fusion_caller_models) CICERO (fusor.fusion_caller_models.Caller attribute) CiceroHarvester (class in fusor.harvester) CiceroTranslator (class in fusor.translator) CIVIC (class in fusor.fusion_caller_models) (fusor.fusion_caller_models.KnowledgebaseList attribute) CIVICHarvester (class in fusor.harvester) CIVICTranslator (class in fusor.translator) CIVICTranslator.Direction (class in fusor.translator) classification (fusor.fusion_caller_models.JAFFA attribute) column_rename (fusor.harvester.ArribaHarvester attribute) (fusor.harvester.CiceroHarvester attribute) (fusor.harvester.EnFusionHarvester attribute) (fusor.harvester.FusionCallerHarvester attribute) (fusor.harvester.FusionCatcherHarvester attribute) (fusor.harvester.GenieHarvester attribute) (fusor.harvester.JAFFAHarvester attribute) (fusor.harvester.StarFusionHarvester attribute) confidence (fusor.fusion_caller_models.Arriba attribute) contig (fusor.fusion_caller_models.Cicero attribute) (fusor.models.AssayedFusion attribute) (fusor.models.ContigSequence attribute) (fusor.models.InternalTandemDuplication attribute) CONTIG_SEQUENCE (fusor.models.FUSORTypes attribute) ContigSequence (class in fusor.models) cool_seq_tool (fusor.tools.FusorDataResourceStatus attribute) coordinate_type (fusor.harvester.ArribaHarvester attribute) (fusor.harvester.CiceroHarvester attribute) (fusor.harvester.EnFusionHarvester attribute) (fusor.harvester.FusionCallerHarvester attribute) (fusor.harvester.FusionCatcherHarvester attribute) (fusor.harvester.GenieHarvester attribute) (fusor.harvester.JAFFAHarvester attribute) (fusor.harvester.StarFusionHarvester attribute) coverage (fusor.models.TranscriptSegmentElement attribute) coverage1 (fusor.fusion_caller_models.Arriba attribute) coverage2 (fusor.fusion_caller_models.Arriba attribute) coverage_3prime (fusor.fusion_caller_models.Cicero attribute) coverage_5prime (fusor.fusion_caller_models.Cicero attribute) criticalFunctionalDomains (fusor.models.CategoricalFusion attribute) (fusor.models.InternalTandemDuplication attribute) D delimiter (fusor.harvester.ArribaHarvester attribute) (fusor.harvester.CiceroHarvester attribute) (fusor.harvester.EnFusionHarvester attribute) (fusor.harvester.FusionCallerHarvester attribute) (fusor.harvester.FusionCatcherHarvester attribute) (fusor.harvester.GenieHarvester attribute) (fusor.harvester.JAFFAHarvester attribute) (fusor.harvester.StarFusionHarvester attribute) direction1 (fusor.fusion_caller_models.Arriba attribute) direction2 (fusor.fusion_caller_models.Arriba attribute) discordant_mates (fusor.fusion_caller_models.Arriba attribute) DomainStatus (class in fusor.models) DuplicationType (class in fusor.models) E elementGenomicEnd (fusor.models.TranscriptSegmentElement attribute) elementGenomicStart (fusor.models.TranscriptSegmentElement attribute) empty_string_to_none() (fusor.fusion_caller_models.Genie class method) enforce_abc() (fusor.models.AbstractFusion class method) (fusor.models.AbstractTranscriptStructuralVariant class method) enforce_element_quantities() (fusor.models.AbstractFusion method) enforce_itd_element_quantities() (fusor.models.InternalTandemDuplication method) EnFusion (class in fusor.fusion_caller_models) ENFUSION (fusor.fusion_caller_models.Caller attribute) EnFusionHarvester (class in fusor.harvester) EnFusionTranslator (class in fusor.translator) ENHANCER (fusor.models.RegulatoryClass attribute) ENHANCER_BLOCKING_ELEMENT (fusor.models.RegulatoryClass attribute) ensure_min_values() (fusor.models.RegulatoryElement method) event_type (fusor.fusion_caller_models.Arriba attribute) (fusor.fusion_caller_models.Cicero attribute) eventDescription (fusor.models.CausativeEvent attribute) EventType (class in fusor.models) eventType (fusor.models.CausativeEvent attribute) Evidence (class in fusor.models) exonEnd (fusor.models.TranscriptSegmentElement attribute) exonEndOffset (fusor.models.TranscriptSegmentElement attribute) exonStart (fusor.models.TranscriptSegmentElement attribute) exonStartOffset (fusor.models.TranscriptSegmentElement attribute) extensions (fusor.models.CategoricalFusion attribute) F featureId (fusor.models.RegulatoryElement attribute) featureLocation (fusor.models.RegulatoryElement attribute) five_prime_end_exon_coords (fusor.fusion_caller_models.CIVIC attribute) five_prime_fusion_point (fusor.fusion_caller_models.FusionCatcher attribute) five_prime_partner (fusor.fusion_caller_models.FusionCatcher attribute) fivePrimeJunction (fusor.models.AbstractTranscriptStructuralVariant attribute) fragmentCoverage (fusor.models.BreakpointCoverage attribute) FUNCTIONAL_DOMAIN (fusor.models.FUSORTypes attribute) functional_domain() (fusor.fusor.FUSOR method) FunctionalDomain (class in fusor.models) fusion() (fusor.fusor.FUSOR method) fusion_caller (fusor.harvester.ArribaHarvester attribute) (fusor.harvester.CiceroHarvester attribute) (fusor.harvester.EnFusionHarvester attribute) (fusor.harvester.FusionCallerHarvester attribute) (fusor.harvester.FusionCatcherHarvester attribute) (fusor.harvester.GenieHarvester attribute) (fusor.harvester.JAFFAHarvester attribute) (fusor.harvester.StarFusionHarvester attribute) FUSION_CATCHER (fusor.fusion_caller_models.Caller attribute) fusion_genes (fusor.fusion_caller_models.JAFFA attribute) fusion_junction_sequence (fusor.fusion_caller_models.EnFusion attribute) fusion_sequence (fusor.fusion_caller_models.FusionCatcher attribute) fusion_transcript (fusor.fusion_caller_models.Arriba attribute) FusionCaller (class in fusor.fusion_caller_models) FusionCallerHarvester (class in fusor.harvester) FusionCallerRecord (class in fusor.harvester) FusionCatcher (class in fusor.fusion_caller_models) FusionCatcherHarvester (class in fusor.harvester) FusionCatcherTranslator (class in fusor.translator) fusionDetection (fusor.models.Assay attribute) FusionKnowledgebase (class in fusor.fusion_caller_models) FusionType (class in fusor.models) FUSOR (class in fusor.fusor) fusor.exceptions module fusor.fusion_caller_models module fusor.fusor module fusor.harvester module fusor.models module fusor.nomenclature module fusor.tools module fusor.translator module FusorDataResourceStatus (class in fusor.tools) FUSORParametersException FUSORTypes (class in fusor.models) G GC_SIGNAL (fusor.models.RegulatoryClass attribute) gene (fusor.models.GeneElement attribute) (fusor.models.TranscriptSegmentElement attribute) gene1 (fusor.fusion_caller_models.Arriba attribute) gene2 (fusor.fusion_caller_models.Arriba attribute) gene_3prime (fusor.fusion_caller_models.Cicero attribute) (fusor.fusion_caller_models.EnFusion attribute) (fusor.translator.GeneFusionPartners attribute) gene_3prime_element (fusor.translator.GeneFusionPartners attribute) gene_5prime (fusor.fusion_caller_models.Cicero attribute) (fusor.fusion_caller_models.EnFusion attribute) (fusor.translator.GeneFusionPartners attribute) gene_5prime_element (fusor.translator.GeneFusionPartners attribute) GENE_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) gene_element() (fusor.fusor.FUSOR method) gene_nomenclature() (in module fusor.nomenclature) gene_normalizer (fusor.tools.FusorDataResourceStatus attribute) GeneElement (class in fusor.models) GeneFusionPartners (class in fusor.translator) generate_nomenclature() (fusor.fusor.FUSOR method) (in module fusor.nomenclature) Genie (class in fusor.fusion_caller_models) GENIE (fusor.fusion_caller_models.Caller attribute) GenieHarvester (class in fusor.harvester) GenieTranslator (class in fusor.translator) GenomicLocation (class in fusor.models) get_error_message() (in module fusor.tools) H harvest_records() (fusor.harvester.FusionCallerHarvester method) I id (fusor.models.FunctionalDomain attribute) IDTranslationException IMPRINTING_CONTROL_REGION (fusor.models.RegulatoryClass attribute) INFERRED (fusor.models.Evidence attribute) inframe (fusor.fusion_caller_models.JAFFA attribute) INSULATOR (fusor.models.RegulatoryClass attribute) INTERNAL_TANDEM_DUPLICATION (fusor.models.DuplicationType attribute) (fusor.models.FUSORTypes attribute) internal_tandem_duplication() (fusor.fusor.FUSOR static method) InternalTandemDuplication (class in fusor.models) J JAFFA (class in fusor.fusion_caller_models) (fusor.fusion_caller_models.Caller attribute) JAFFAHarvester (class in fusor.harvester) JAFFATranslator (class in fusor.translator) junction_read_count (fusor.fusion_caller_models.STARFusion attribute) K KnowledgebaseList (class in fusor.fusion_caller_models) L label (fusor.models.FunctionalDomain attribute) left_breakpoint (fusor.fusion_caller_models.STARFusion attribute) left_gene (fusor.fusion_caller_models.STARFusion attribute) linker_element() (fusor.fusor.FUSOR static method) LINKER_SEQUENCE_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) LinkerElement (class in fusor.models) linkerSequence (fusor.models.LinkerElement attribute) load_record_table() (fusor.harvester.FusionCallerHarvester method) load_records() (fusor.harvester.CIVICHarvester method) (fusor.harvester.FusionCallerHarvester method) (fusor.harvester.MOAHarvester method) LOCATION_ID (fusor.models.AdditionalFields attribute) LOCUS_CONTROL_REGION (fusor.models.RegulatoryClass attribute) LOST (fusor.models.DomainStatus attribute) M methodUri (fusor.models.Assay attribute) MINUS_10_SIGNAL (fusor.models.RegulatoryClass attribute) MINUS_35_SIGNAL (fusor.models.RegulatoryClass attribute) MOA (fusor.fusion_caller_models.KnowledgebaseList attribute) MOAHarvester (class in fusor.harvester) MOATranslator (class in fusor.translator) module fusor.exceptions fusor.fusion_caller_models fusor.fusor fusor.harvester fusor.models fusor.nomenclature fusor.tools fusor.translator molecular_profiles (fusor.fusion_caller_models.CIVIC attribute) MULTIPLE_POSSIBLE_GENES_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) multiple_possible_genes_element() (fusor.fusor.FUSOR static method) MultiplePossibleGenesElement (class in fusor.models) N name (fusor.models.GenomicLocation attribute) NEGATIVE (fusor.translator.CIVICTranslator.Direction attribute) O OBSERVED (fusor.models.Evidence attribute) OTHER (fusor.models.RegulatoryClass attribute) P paired_end_reads (fusor.fusion_caller_models.Genie attribute) POLYA_SIGNAL_SEQUENCE (fusor.models.RegulatoryClass attribute) pos_3prime (fusor.fusion_caller_models.Cicero attribute) pos_5prime (fusor.fusion_caller_models.Cicero attribute) POSITIVE (fusor.translator.CIVICTranslator.Direction attribute) predicted_effect (fusor.fusion_caller_models.FusionCatcher attribute) PRESERVED (fusor.models.DomainStatus attribute) PROMOTER (fusor.models.RegulatoryClass attribute) R READ_DATA (fusor.models.FUSORTypes attribute) READ_THROUGH (fusor.models.EventType attribute) ReadData (class in fusor.models) readData (fusor.models.AssayedFusion attribute) (fusor.models.InternalTandemDuplication attribute) reading_frame (fusor.fusion_caller_models.Genie attribute) readingFramePreserved (fusor.models.AbstractTranscriptStructuralVariant attribute) reads (fusor.models.AnchoredReads attribute) reads_3prime (fusor.fusion_caller_models.Cicero attribute) reads_5prime (fusor.fusion_caller_models.Cicero attribute) rearrangement (fusor.fusion_caller_models.JAFFA attribute) REARRANGEMENT (fusor.models.EventType attribute) reg_element_nomenclature() (in module fusor.nomenclature) region (fusor.models.TemplatedSequenceElement attribute) REGULATORY_ELEMENT (fusor.models.FUSORTypes attribute) regulatory_element() (fusor.fusor.FUSOR method) RegulatoryClass (class in fusor.models) regulatoryClass (fusor.models.RegulatoryElement attribute) RegulatoryElement (class in fusor.models) regulatoryElement (fusor.models.AbstractTranscriptStructuralVariant attribute) RESPONSE_ELEMENT (fusor.models.RegulatoryClass attribute) rf (fusor.fusion_caller_models.Arriba attribute) RIBOSOME_BINDING_SITE (fusor.models.RegulatoryClass attribute) RIBOSWITCH (fusor.models.RegulatoryClass attribute) right_breakpoint (fusor.fusion_caller_models.STARFusion attribute) right_gene (fusor.fusion_caller_models.STARFusion attribute) S save_fusions_cache() (in module fusor.models) SEQUENCE_ID (fusor.models.AdditionalFields attribute) sequenceLocation (fusor.models.FunctionalDomain attribute) SILENCER (fusor.models.RegulatoryClass attribute) site1_chrom (fusor.fusion_caller_models.Genie attribute) site1_hugo (fusor.fusion_caller_models.Genie attribute) site1_pos (fusor.fusion_caller_models.Genie attribute) site2_chrom (fusor.fusion_caller_models.Genie attribute) site2_hugo (fusor.fusion_caller_models.Genie attribute) site2_pos (fusor.fusion_caller_models.Genie attribute) source (fusor.harvester.FusionCallerRecord attribute) spanning (fusor.models.ReadData attribute) spanning_frag_count (fusor.fusion_caller_models.STARFusion attribute) spanning_pairs (fusor.fusion_caller_models.JAFFA attribute) spanning_reads (fusor.fusion_caller_models.FusionCatcher attribute) (fusor.fusion_caller_models.JAFFA attribute) SPANNING_READS (fusor.models.FUSORTypes attribute) spanning_unique_reads (fusor.fusion_caller_models.FusionCatcher attribute) SpanningReads (class in fusor.models) spanningReads (fusor.models.SpanningReads attribute) split (fusor.models.ReadData attribute) split_reads (fusor.fusion_caller_models.Genie attribute) SPLIT_READS (fusor.models.FUSORTypes attribute) split_reads1 (fusor.fusion_caller_models.Arriba attribute) split_reads2 (fusor.fusion_caller_models.Arriba attribute) SplitReads (class in fusor.models) splitReads (fusor.models.SplitReads attribute) STAR_FUSION (fusor.fusion_caller_models.Caller attribute) STARFusion (class in fusor.fusion_caller_models) StarFusionHarvester (class in fusor.harvester) STARFusionTranslator (class in fusor.translator) status (fusor.models.FunctionalDomain attribute) strand (fusor.models.TemplatedSequenceElement attribute) (fusor.models.TranscriptSegmentElement attribute) strand1 (fusor.fusion_caller_models.Arriba attribute) strand2 (fusor.fusion_caller_models.Arriba attribute) StructuralElementType (class in fusor.models) structure (fusor.models.AbstractTranscriptStructuralVariant attribute) (fusor.models.AssayedFusion attribute) (fusor.models.CategoricalFusion attribute) (fusor.models.InternalTandemDuplication attribute) structure_ends() (fusor.models.AbstractFusion method) sv_ort (fusor.fusion_caller_models.Cicero attribute) T TATA_BOX (fusor.models.RegulatoryClass attribute) templated_seq_nomenclature() (in module fusor.nomenclature) TEMPLATED_SEQUENCE_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) templated_sequence_element() (fusor.fusor.FUSOR method) TemplatedSequenceElement (class in fusor.models) TERMINATOR (fusor.models.RegulatoryClass attribute) three_prime_fusion_point (fusor.fusion_caller_models.FusionCatcher attribute) three_prime_partner (fusor.fusion_caller_models.FusionCatcher attribute) three_prime_start_exon_coords (fusor.fusion_caller_models.CIVIC attribute) threePrimeJunction (fusor.models.AbstractTranscriptStructuralVariant attribute) TRANS_SPLICING (fusor.models.EventType attribute) transcript (fusor.models.TranscriptSegmentElement attribute) TRANSCRIPT_SEGMENT_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) transcript_segment_element() (fusor.fusor.FUSOR method) TranscriptSegmentElement (class in fusor.models) transcriptStatus (fusor.models.TranscriptSegmentElement attribute) translate() (fusor.harvester.FusionCallerHarvester method) (fusor.translator.ArribaTranslator method) (fusor.translator.CiceroTranslator method) (fusor.translator.CIVICTranslator method) (fusor.translator.EnFusionTranslator method) (fusor.translator.FusionCatcherTranslator method) (fusor.translator.GenieTranslator method) (fusor.translator.JAFFATranslator method) (fusor.translator.MOATranslator method) (fusor.translator.STARFusionTranslator method) (fusor.translator.Translator method) Translator (class in fusor.translator) translator_class (fusor.harvester.ArribaHarvester attribute) (fusor.harvester.CiceroHarvester attribute) (fusor.harvester.CIVICHarvester attribute) (fusor.harvester.EnFusionHarvester attribute) (fusor.harvester.FusionCallerHarvester attribute) (fusor.harvester.FusionCatcherHarvester attribute) (fusor.harvester.GenieHarvester attribute) (fusor.harvester.JAFFAHarvester attribute) (fusor.harvester.MOAHarvester attribute) (fusor.harvester.StarFusionHarvester attribute) tx_segment_nomenclature() (in module fusor.nomenclature) type (fusor.fusion_caller_models.Arriba attribute) (fusor.fusion_caller_models.Cicero attribute) (fusor.fusion_caller_models.CIVIC attribute) (fusor.fusion_caller_models.EnFusion attribute) (fusor.fusion_caller_models.FusionCaller attribute) (fusor.fusion_caller_models.FusionCatcher attribute) (fusor.fusion_caller_models.FusionKnowledgebase attribute) (fusor.fusion_caller_models.Genie attribute) (fusor.fusion_caller_models.JAFFA attribute) (fusor.fusion_caller_models.STARFusion attribute) (fusor.models.AbstractFusion attribute) (fusor.models.AnchoredReads attribute) (fusor.models.Assay attribute) (fusor.models.AssayedFusion attribute) (fusor.models.BaseStructuralElement attribute) (fusor.models.BreakpointCoverage attribute) (fusor.models.CategoricalFusion attribute) (fusor.models.CausativeEvent attribute) (fusor.models.ContigSequence attribute) (fusor.models.FunctionalDomain attribute) (fusor.models.GeneElement attribute) (fusor.models.InternalTandemDuplication attribute) (fusor.models.LinkerElement attribute) (fusor.models.MultiplePossibleGenesElement attribute) (fusor.models.ReadData attribute) (fusor.models.RegulatoryElement attribute) (fusor.models.SpanningReads attribute) (fusor.models.SplitReads attribute) (fusor.models.TemplatedSequenceElement attribute) (fusor.models.TranscriptSegmentElement attribute) (fusor.models.UnknownGeneElement attribute) U UNKNOWN_GENE_ELEMENT (fusor.models.FUSORTypes attribute) (fusor.models.StructuralElementType attribute) unknown_gene_element() (fusor.fusor.FUSOR static method) UnknownGeneElement (class in fusor.models) V validate_genomic_location() (fusor.models.GenomicLocation class method) values() (fusor.models.DuplicationType class method) (fusor.models.FusionType class method) vicc_compliant_name (fusor.fusion_caller_models.CIVIC attribute) viccNomenclature (fusor.models.AbstractFusion attribute)