fusor.transcript_junction_builder

Module for easy generation of FUSOR AssayedFusion/CategoricalFusion objects

class fusor.transcript_junction_builder.TranscriptJunctionBuilder(fusor, five_prime_gene, three_prime_gene, five_prime_reference_sequence=None, three_prime_reference_sequence=None, annotation_type=None, five_prime_junction=0, three_prime_junction=0, five_prime_intronic_offset=0, three_prime_intronic_offset=0, linker_sequence=None, assayed_fusion=True)[source]

Class for quick FUSOR object generation

__init__(fusor, five_prime_gene, three_prime_gene, five_prime_reference_sequence=None, three_prime_reference_sequence=None, annotation_type=None, five_prime_junction=0, three_prime_junction=0, five_prime_intronic_offset=0, three_prime_intronic_offset=0, linker_sequence=None, assayed_fusion=True)[source]

Initialize TranscriptJunctionBuilder class

Parameters:

  • fusor (FUSOR) – A FUSOR object

  • five_prime_gene (str) – The 5’ gene partner

  • three_prime_gene (str) – The 3’ gene partner

  • five_prime_reference_sequence (Optional[str]) – The 5’ prime reference sequence, either transcript or genomic. By default, this is set to None

  • three_prime_reference_sequence (Optional[str]) – The 5’ prime reference sequence, either transcript or genomic. By default, this is set to None

  • annotation_type (Optional[AnnotationLayer]) – The annotation type describing the 5’ and 3’ reference sequences. This should be set to either c. or g. By default, this is set to None

  • five_prime_junction (int) – The 5’ junction location, described using a residue coordinate (1-based) on a transcript or genomic sequence. By default, this is set to 0.

  • three_prime_junction (int) – The 3’ junction location, described using a residue coordinate (1-based) on a transcript or genomic sequence. By default, this is set to 0.

  • five_prime_intronic_offset (int) – The intronic offset for the 5’ junction, described using a residue coordinate (1-based) on a transcript sequence. By default, this is set to 0.

  • three_prime_intronic_offset (int) – The intronic offset for the 5’ junction, described using a residue coordinate (1-based) on a transcript sequence. By default, this is set to 0.

  • linker_sequence (Optional[str]) – The linker sequence. By default, this is set to None

  • assayed_fusion (bool) – If an AssayedFusion object should be created. By default, this is set to True.

Raises:

ValueError – If five_prime_junction or three_prime_junction are not described using c. or g. coordinates

async build_fusion()[source]

Create AssayedFusion or CategoricalFusion in user-accessible way

Return type:

AssayedFusion | CategoricalFusion

Returns:

An AssayedFusion or CategoricalFusion object