fusor.fusion_caller_models
Schemas for outputs provided by different fusion callers
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class fusor.fusion_caller_models.Arriba(**data)[source]
Define parameters for Arriba model
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breakpoint1:
str[source]
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breakpoint2:
str[source]
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confidence:
str[source]
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coverage1:
int[source]
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coverage2:
int[source]
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direction1:
str[source]
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direction2:
str[source]
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discordant_mates:
int[source]
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event_type:
str[source]
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fusion_transcript:
str[source]
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gene1:
str[source]
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gene2:
str[source]
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rf:
str[source]
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split_reads1:
int[source]
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split_reads2:
int[source]
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strand1:
str[source]
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strand2:
str[source]
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type:
Literal[<Caller.ARRIBA: 'Arriba'>][source]
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class fusor.fusion_caller_models.CIVIC(**data)[source]
Define parameters for CIVIC model
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five_prime_end_exon_coords:
Optional[ExonCoordinate][source]
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molecular_profiles:
Optional[list[MolecularProfile]][source]
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three_prime_start_exon_coords:
Optional[ExonCoordinate][source]
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type:
Literal[<KnowledgebaseList.CIVIC: 'CIVIC'>][source]
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vicc_compliant_name:
str[source]
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class fusor.fusion_caller_models.Caller(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
Define different supported callers
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ARRIBA = 'Arriba'[source]
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CICERO = 'CICERO'[source]
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ENFUSION = 'EnFusion'[source]
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FUSION_CATCHER = 'FusionCatcher'[source]
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GENIE = 'GENIE'[source]
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JAFFA = 'JAFFA'[source]
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STAR_FUSION = 'STAR-Fusion'[source]
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class fusor.fusion_caller_models.Cicero(**data)[source]
Define parameters for CICERO model
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chr_3prime:
str[source]
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chr_5prime:
str[source]
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contig:
str[source]
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coverage_3prime:
int[source]
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coverage_5prime:
int[source]
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event_type:
str[source]
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gene_3prime:
str[source]
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gene_5prime:
str[source]
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pos_3prime:
int[source]
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pos_5prime:
int[source]
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reads_3prime:
int[source]
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reads_5prime:
int[source]
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sv_ort:
str[source]
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type:
Literal[<Caller.CICERO: 'CICERO'>][source]
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class fusor.fusion_caller_models.EnFusion(**data)[source]
Define parameters for EnFusion model
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break_3prime:
int[source]
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break_5prime:
int[source]
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chr_3prime:
int | str[source]
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chr_5prime:
int | str[source]
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fusion_junction_sequence:
Optional[str][source]
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gene_3prime:
str[source]
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gene_5prime:
str[source]
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type:
Literal[<Caller.ENFUSION: 'EnFusion'>][source]
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class fusor.fusion_caller_models.FusionCaller(**data)[source]
ABC for fusion callers
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type:
Caller[source]
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class fusor.fusion_caller_models.FusionCatcher(**data)[source]
Define parameters for FusionCatcher model
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five_prime_fusion_point:
str[source]
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five_prime_partner:
str[source]
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fusion_sequence:
str[source]
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predicted_effect:
str[source]
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spanning_reads:
int[source]
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spanning_unique_reads:
int[source]
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three_prime_fusion_point:
str[source]
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three_prime_partner:
str[source]
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type:
Literal[<Caller.FUSION_CATCHER: 'FusionCatcher'>][source]
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class fusor.fusion_caller_models.FusionKnowledgebase(**data)[source]
ABC for Fusion Knowledgebases
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type:
KnowledgebaseList[source]
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class fusor.fusion_caller_models.Genie(**data)[source]
Define parameters for Genie model
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annot:
str[source]
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reading_frame:
str[source]
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site1_chrom:
int[source]
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site1_hugo:
str[source]
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site1_pos:
int[source]
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site2_chrom:
int[source]
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site2_hugo:
str[source]
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site2_pos:
int[source]
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type:
Literal[<Caller.GENIE: 'GENIE'>][source]
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class fusor.fusion_caller_models.JAFFA(**data)[source]
Define parameters for JAFFA model
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base1:
int[source]
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base2:
int[source]
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chrom1:
str[source]
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chrom2:
str[source]
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classification:
str[source]
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fusion_genes:
str[source]
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inframe:
bool | str[source]
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rearrangement:
bool[source]
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spanning_pairs:
int[source]
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spanning_reads:
int[source]
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type:
Literal[<Caller.JAFFA: 'JAFFA'>][source]
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class fusor.fusion_caller_models.KnowledgebaseList(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]
Define supported knowledgebases
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CIVIC = 'CIVIC'[source]
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MOA = 'MOA'[source]
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class fusor.fusion_caller_models.STARFusion(**data)[source]
Define parameters for STAR-Fusion model
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annots:
str[source]
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junction_read_count:
int[source]
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left_breakpoint:
str[source]
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left_gene:
str[source]
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right_breakpoint:
str[source]
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right_gene:
str[source]
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spanning_frag_count:
int[source]
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type:
Literal[<Caller.STAR_FUSION: 'STAR-Fusion'>][source]