fusor.fusion_caller_models

Schemas for outputs provided by different fusion callers

class fusor.fusion_caller_models.Arriba(**data)[source]

Define parameters for Arriba model

breakpoint1: str[source]
breakpoint2: str[source]
confidence: str[source]
coverage1: int[source]
coverage2: int[source]
direction1: str[source]
direction2: str[source]
discordant_mates: int[source]
event_type: str[source]
fusion_transcript: str[source]
gene1: str[source]
gene2: str[source]
rf: str[source]
split_reads1: int[source]
split_reads2: int[source]
strand1: str[source]
strand2: str[source]
type: Literal[<Caller.ARRIBA: 'Arriba'>][source]
class fusor.fusion_caller_models.CIVIC(**data)[source]

Define parameters for CIVIC model

five_prime_end_exon_coords: Optional[ExonCoordinate][source]
molecular_profiles: Optional[list[MolecularProfile]][source]
three_prime_start_exon_coords: Optional[ExonCoordinate][source]
type: Literal[<KnowledgebaseList.CIVIC: 'CIVIC'>][source]
vicc_compliant_name: str[source]
class fusor.fusion_caller_models.Caller(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

Define different supported callers

ARRIBA = 'Arriba'[source]
CICERO = 'CICERO'[source]
ENFUSION = 'EnFusion'[source]
FUSION_CATCHER = 'FusionCatcher'[source]
FUSION_MAP = 'FusionMap'[source]
GENIE = 'GENIE'[source]
JAFFA = 'JAFFA'[source]
MAPSPLICE = 'MapSplice'[source]
STAR_FUSION = 'STAR-Fusion'[source]
class fusor.fusion_caller_models.Cicero(**data)[source]

Define parameters for CICERO model

chr_3prime: str[source]
chr_5prime: str[source]
contig: str[source]
coverage_3prime: int[source]
coverage_5prime: int[source]
event_type: str[source]
gene_3prime: str[source]
gene_5prime: str[source]
pos_3prime: int[source]
pos_5prime: int[source]
reads_3prime: int[source]
reads_5prime: int[source]
sv_ort: str[source]
type: Literal[<Caller.CICERO: 'CICERO'>][source]
class fusor.fusion_caller_models.EnFusion(**data)[source]

Define parameters for EnFusion model

break_3prime: int[source]
break_5prime: int[source]
chr_3prime: int | str[source]
chr_5prime: int | str[source]
fusion_junction_sequence: Optional[str][source]
gene_3prime: str[source]
gene_5prime: str[source]
type: Literal[<Caller.ENFUSION: 'EnFusion'>][source]
class fusor.fusion_caller_models.FusionCaller(**data)[source]

ABC for fusion callers

type: Caller[source]
class fusor.fusion_caller_models.FusionCatcher(**data)[source]

Define parameters for FusionCatcher model

five_prime_fusion_point: str[source]
five_prime_partner: str[source]
fusion_sequence: str[source]
predicted_effect: str[source]
spanning_reads: int[source]
spanning_unique_reads: int[source]
three_prime_fusion_point: str[source]
three_prime_partner: str[source]
type: Literal[<Caller.FUSION_CATCHER: 'FusionCatcher'>][source]
class fusor.fusion_caller_models.FusionKnowledgebase(**data)[source]

ABC for Fusion Knowledgebases

type: KnowledgebaseList[source]
class fusor.fusion_caller_models.Genie(**data)[source]

Define parameters for Genie model

annot: str[source]
reading_frame: str[source]
site1_chrom: int[source]
site1_hugo: str[source]
site1_pos: int[source]
site2_chrom: int[source]
site2_hugo: str[source]
site2_pos: int[source]
type: Literal[<Caller.GENIE: 'GENIE'>][source]
class fusor.fusion_caller_models.JAFFA(**data)[source]

Define parameters for JAFFA model

base1: int[source]
base2: int[source]
chrom1: str[source]
chrom2: str[source]
classification: str[source]
fusion_genes: str[source]
inframe: bool | str[source]
rearrangement: bool[source]
spanning_pairs: int[source]
spanning_reads: int[source]
type: Literal[<Caller.JAFFA: 'JAFFA'>][source]
class fusor.fusion_caller_models.KnowledgebaseList(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]

Define supported knowledgebases

CIVIC = 'CIVIC'[source]
class fusor.fusion_caller_models.STARFusion(**data)[source]

Define parameters for STAR-Fusion model

annots: str[source]
junction_read_count: int[source]
left_breakpoint: str[source]
left_gene: str[source]
right_breakpoint: str[source]
right_gene: str[source]
spanning_frag_count: int[source]
type: Literal[<Caller.STAR_FUSION: 'STAR-Fusion'>][source]