fusor.translator

Module for translating output from fusion detection methods to fusion objects (AssayedFusion/CategoricalFusion)

class fusor.translator.ArribaTranslator(fusor)

Initialize ArribaTranslator class

async translate(arriba, coordinate_type, rb)

Parse Arriba output to create AssayedFusion object

Parameters:

• arriba (Arriba) – Output from Arriba caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.CIVICTranslator(fusor)

Initialize CIVICTranslator

class Direction(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define CIViC-specific enum for transcript direction

NEGATIVE = 'NEGATIVE'

POSITIVE = 'POSITIVE'

async translate(civic)

Convert CIViC record to Categorical Fusion

:param civic A CIVIC object :rtype: CategoricalFusion

:return A CategoricalFusion object, if construction is successful :raises: ValueError if a transcript accession and exon number is

provided without corresponding genomic breakpoints

class fusor.translator.CiceroTranslator(fusor)

Initialize CiceroTranslator class

async translate(cicero, coordinate_type, rb)

Parse CICERO output to create AssayedFusion object

Parameters:

• cicero (Cicero) – Output from CICERO caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion | str

Returns:

An AssayedFusion object, if construction is successful

Raises:

RuntimeError – If CICERO annotations indicate the fusion is not valid

class fusor.translator.EnFusionTranslator(fusor)

Initialize EnFusionTranslator class

async translate(enfusion, coordinate_type, rb)

Parse EnFusion output to create AssayedFusion object

Parameters:

• enfusion (EnFusion) – Output from EnFusion caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.FusionCatcherTranslator(fusor)

Initialize FusionCatcherTranslator class

async translate(fusion_catcher, coordinate_type, rb)

Parse FusionCatcher output to create AssayedFusion object

Parameters:

• fusion_catcher (FusionCatcher) – Output from FusionCatcher caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.GeneFusionPartners(**data)

Class for defining gene fusion partners

gene_3prime: Optional[str]

gene_3prime_element: GeneElement | UnknownGeneElement | MultiplePossibleGenesElement

gene_5prime: Optional[str]

gene_5prime_element: GeneElement | UnknownGeneElement | MultiplePossibleGenesElement

class fusor.translator.GenieTranslator(fusor)

Initialize GenieTranslator class

async translate(genie, coordinate_type, rb)

Parse GENIE output to create AssayedFusion object

Parameters:

• genie (Genie) – Output from GENIE dataset

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.JAFFATranslator(fusor)

Initialize JAFFATranslator class

async translate(jaffa, coordinate_type, rb)

Parse JAFFA fusion output to create AssayedFusion object

Parameters:

• JAFFA – Output from JAFFA caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

Optional[AssayedFusion]

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.MOATranslator(fusor)

Initialize MOATranslator

translate(moa_assertion)

Convert a MOA assertion to a CategoricalFusion object

Parameters:

moa_assertion (dict) – A dictionary representing a MOA assertion. To note, MOA fusions do not report genomic breakpoints. Currently, we only support fusions where both partners are listed, as we cannot definitively determine for cases where one gene symbol is provided if it describes the 5’ or 3’ partner.

Return type:

CategoricalFusion

Returns:

A CategoricalFusion object

class fusor.translator.STARFusionTranslator(fusor)

Initialize STARFusionTranslator class

async translate(star_fusion, coordinate_type, rb)

Parse STAR-Fusion output to create AssayedFusion object

Parameters:

• star_fusion (STARFusion) – Output from STAR-Fusion caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

class fusor.translator.Translator(fusor)

Class for translating outputs from different fusion detection algorithms to FUSOR AssayedFusion and CategoricalFusion objects

__init__(fusor)

Initialize Translator class

Parameters:

fusor (FUSOR) – A FUSOR instance

abstract async translate(fusion_data, coordinate_type, rb)

Define abstract translate method

Parameters:

• fusion_data (BaseModel) – The fusion data from a fusion caller

• coordinate_type (CoordinateType) – If the coordinate is inter-residue or residue

• rb (Assembly) – The reference build used to call the fusion

Return type:

AssayedFusion | CategoricalFusion | InternalTandemDuplication

Returns:

An AssayedFusion or CategoricalFusion object, if construction is successful