fusor.translator

Module for translating output from fusion detection methods to FUSOR AssayedFusion objects

class fusor.translator.GeneFusionPartners(**data)[source]

Class for defining gene fusion partners

gene_3prime: Optional[str][source]
gene_3prime_element: GeneElement | UnknownGeneElement | MultiplePossibleGenesElement[source]
gene_5prime: Optional[str][source]
gene_5prime_element: GeneElement | UnknownGeneElement | MultiplePossibleGenesElement[source]
class fusor.translator.Translator(fusor)[source]

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

__init__(fusor)[source]

Initialize Translator class

Parameters:

fusor (FUSOR) – A FUSOR instance

async from_arriba(arriba, coordinate_type, rb)[source]

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

async from_cicero(cicero, coordinate_type, rb)[source]

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

async from_civic(civic)[source]

Convert CIViC record to Categorical Fusion

:param civic A CIVIC object :return A CategoricalFusion object, if construction is successful

Return type:

CategoricalFusion

async from_enfusion(enfusion, coordinate_type, rb)[source]

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

async from_fusion_catcher(fusion_catcher, coordinate_type, rb)[source]

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

async from_fusion_map(fmap_row, coordinate_type, rb)[source]

Parse FusionMap output to create FUSOR AssayedFusion object

Parameters:

  • fmap_row (DataFrame) – A row of FusionMap output

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

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

Return type:

AssayedFusion

Returns:

An AssayedFusion object, if construction is successful

async from_genie(genie, coordinate_type, rb)[source]

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

async from_jaffa(jaffa, coordinate_type, rb)[source]

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

async from_mapsplice(mapsplice_row, coordinate_type, rb)[source]

Parse MapSplice output to create AssayedFusion object

Parameters:

  • mapsplice_row (DataFrame) – A row of MapSplice output

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

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

Retun:

An AssayedFusion object, if construction is successful

Return type:

AssayedFusion

async from_star_fusion(star_fusion, coordinate_type, rb)[source]

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