fusor.fusor

Module for modifying fusion objects.

class fusor.fusor.FUSOR(gene_database=None, cool_seq_tool=None)

Class for modifying fusion objects.

__init__(gene_database=None, cool_seq_tool=None)

Initialize FUSOR class.

Parameters:

• cool_seq_tool (Optional[CoolSeqTool]) – Cool-Seq-Tool instance

• gene_database (Optional[AbstractDatabase]) – gene normalizer database instance

static assayed_fusion(structure, causative_event=None, assay=None, regulatory_element=None, reading_frame_preserved=None)

Construct an AssayedFusion object.

Parameters:

• structure (list[TranscriptSegmentElement | GeneElement | TemplatedSequenceElement | LinkerElement | UnknownGeneElement | ContigSequence | ReadData]) – elements constituting the fusion

• causative_event (Optional[CausativeEvent]) – event causing the fusion

• assay (Optional[Assay]) – how knowledge of the fusion was obtained

• regulatory_element (Optional[RegulatoryElement]) – affected regulatory elements

• reading_frame_preserved (Optional[bool]) – True if reading frame is preserved. False otherwise.

Return type:

AssayedFusion

Returns:

Tuple containing optional AssayedFusion if construction successful, and any relevant validation warnings

static categorical_fusion(structure, regulatory_element=None, critical_functional_domains=None, reading_frame_preserved=None)

Construct a CategoricalFusion object

Parameters:

• structure (list[TranscriptSegmentElement | GeneElement | TemplatedSequenceElement | LinkerElement | MultiplePossibleGenesElement]) – elements constituting the fusion

• regulatory_element (Optional[RegulatoryElement]) – affected regulatory element

• critical_functional_domains (Optional[list[FunctionalDomain]]) – lost or preserved functional domains

• reading_frame_preserved (Optional[bool]) – True if reading frame is preserved. False otherwise

Return type:

CategoricalFusion

Returns:

CategoricalFusion if construction successful

Raise:

FUSORParametersException if given incorrect fusion properties

functional_domain(status, name, functional_domain_id, gene, sequence_id, start, end, use_minimal_gene=True, coordinate_type=CoordinateType.RESIDUE, seq_id_target_namespace=None)

Build FunctionalDomain object.

Parameters:

• status (DomainStatus) – Status for domain. Must be either lost or preserved

• name (str) – Domain name

• functional_domain_id (str) – Domain ID

• gene (str) – Gene

• sequence_id (str) – protein sequence on which provided coordinates are located

• start (int) – start position on sequence

• end (int) – end position on sequence

• use_minimal_gene (bool) – True if minimal gene object (id, label) will be used. False if gene-normalizer’s gene object will be used

• coordinate_type (CoordinateType) – The coordinate type that is being supplied for start and end. This is set to residue coordinates by default

• seq_id_target_namespace (Optional[str]) – If want to use digest for sequence_id, set this to the namespace you want the digest for. Otherwise, leave as None.

Return type:

tuple[Optional[FunctionalDomain], Optional[str]]

Returns:

Tuple with FunctionalDomain and None value for warnings if successful, or a None value and warning message if unsuccessful

fusion(fusion_type=None, **kwargs)

Construct Fusion object.

Fusion type (assayed vs categorical) can be inferred based on provided kwargs, assuming they can sufficiently discriminate the type.

Parameters:

fusion_type (Optional[FusionType]) – explicitly specify fusion type. Unnecessary if providing fusion object in keyword args that includes type attribute.

Return type:

CategoricalFusion | AssayedFusion

Returns:

constructed fusion object if successful

Raise:

FUSORParametersException if fusion type unable to be determined, or if incorrect fusion parameters are provided

gene_element(gene, use_minimal_gene=True)

Create gene element

Parameters:

• gene (str) – The gene symbol name

• use_minimal_gene (bool) – True if minimal gene object (id and label) will be used. False if gene-normalizer’s gene object will be used

Return type:

tuple[Optional[GeneElement], Optional[str]]

Returns:

GeneElement, warning

generate_nomenclature(fusion)

Generate human-readable nomenclature describing provided fusion

Parameters:

fusion (CategoricalFusion | AssayedFusion) – a valid fusion

Return type:

str

Returns:

string summarizing fusion in human-readable way per VICC fusion curation nomenclature

static internal_tandem_duplication(structure, causative_event=None, assay=None, regulatory_element=None, reading_frame_preserved=None, critical_functional_domains=None)

Construct an InternalTandemDuplication (ITD) object

Parameters:

• structure (list[TranscriptSegmentElement | GeneElement | TemplatedSequenceElement | LinkerElement | UnknownGeneElement | MultiplePossibleGenesElement]) – Elements constituting the ITD

• causative_event (Optional[CausativeEvent]) – event causing the fusion

• assay (Optional[Assay]) – how knowledge of the fusion was obtained

• regulatory_element (Optional[RegulatoryElement]) – affected regulatory elements

• critical_functional_domains (Optional[list[FunctionalDomain]]) – lost or preserved functional domains

• reading_frame_preserved (Optional[bool]) – True if reading frame is preserved. False otherwise

Return type:

InternalTandemDuplication

Returns:

InternalTandemDuplication if construction successful

Raise:

FUSORParametersException if given incorrect fusion properties

static linker_element(sequence)

Create linker element

Parameters:

sequence (str) – A nucleotide sequence

Return type:

tuple[Optional[LinkerElement], Optional[str]]

Returns:

Tuple containing a complete Linker element and None if successful, or a None value and warning message if unsuccessful

static multiple_possible_genes_element()

Create a MultiplePossibleGenesElement.

Return type:

MultiplePossibleGenesElement

Returns:

MultiplePossibleGenesElement

regulatory_element(regulatory_class, gene, feature_id=None, sequence_id=None, start=None, end=None, seq_id_target_namespace=None, coordinate_type=CoordinateType.RESIDUE, use_minimal_gene=True)

Create RegulatoryElement

Parameters:

• regulatory_class (RegulatoryClass) – one of {“promoter”, “enhancer”}

• gene (str) – gene term to fetch normalized gene object for

• feature_id (Optional[str]) – The feature ID for the regulatory element

• sequence_id (Optional[str]) – Genomic sequence on which provided coordinates exist

• start (Optional[int]) – Start position on sequence

• end (Optional[int]) – Etart position on sequence

• seq_id_target_namespace (Optional[str]) –

  If want to use digest for sequence_id, set this to the namespace you want the digest for.

  Otherwise, leave as None.

• coordinate_type (CoordinateType) – The coordinate type that is being supplied for start and end. This is set to residue coordinates by default

• use_minimal_gene (bool) – whether to use the minimal gene object

Return type:

tuple[Optional[RegulatoryElement], Optional[str]]

Returns:

Tuple with RegulatoryElement instance and None value for warnings if successful, or a None value and warning message if unsuccessful

templated_sequence_element(start, end, sequence_id, strand, coordinate_type=CoordinateType.INTER_RESIDUE, seq_id_target_namespace=None)

Create templated sequence element

Parameters:

• start (int) – Genomic start

• end (int) – Genomic end

• sequence_id (str) – Chromosome accession for sequence

• strand (Strand) – Strand

• coordinate_type (CoordinateType) – Determines coordinate base used. Must be one of residue or inter-residue. Set to inter-residue by default.

• seq_id_target_namespace (Optional[str]) – If want to use digest for sequence_id, set this to the namespace you want the digest for. Otherwise, leave as None.

Return type:

TemplatedSequenceElement

Returns:

Templated Sequence Element

async transcript_segment_element(tx_to_genomic_coords=True, use_minimal_gene=True, seq_id_target_namespace=None, coverage=None, reads=None, **kwargs)

Create TranscriptSegmentElement.

Parameters:

• tx_to_genomic_coords (bool) – True if going from transcript to genomic coordinates. False if going from genomic to transcript exon coordinates.

• use_minimal_gene (bool) – True if minimal gene object (id, label) will be used. False if gene-normalizer’s entire gene object will be used

• seq_id_target_namespace (Optional[str]) – If want to use digest for sequence_id, set this to the namespace you want the digest for. Otherwise, leave as None.

• coverage (Optional[BreakpointCoverage]) – The read coverage located near the specified breakpoint

• reads (Optional[AnchoredReads]) – The read data for the specified breakpoint

• kwargs –

  If tx_to_genomic_coords, possible key word arguments:

  (From cool_seq_tool.tx_segment_to_genomic)

  • gene (str | None = None)

  • transcript (str | None = None)

  • exon_start (int | None = None)

  • exon_start_offset: Optional[int] = 0

  • exon_end: Optional[int] = None

  • exon_end_offset: (Optional[int] = 0)

  else:

  (From cool_seq_tool.genomic_to_tx_segment)

  • genomic_ac: (str)

  • seg_start_genomic: (Optional[int] = None)

  • seg_end_genomic: (Optional[int] = None)

  • transcript: (Optional[str] = None)

  • gene: (Optional[str] = None)

Return type:

tuple[Optional[TranscriptSegmentElement], Optional[list[str]]]

Returns:

Transcript Segment Element, warning

static unknown_gene_element()

Create UnknownGeneElement

Return type:

UnknownGeneElement

Returns:

UnknownGeneElement