Computable object representation and validation for gene fusions
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FUSOR
Documentation · Installation · Usage · API reference
Overview
FUSOR (FUSion Object Representation) provides modeling and validation tools for representing gene fusions in a precise, computable structure that adheres to the VICC Gene Fusion Specification. It also provides easy access to transcript selection and coordinate conversion tools, and enables generation of human-readable fusion nomenclature.
Install
FUSOR is available on PyPI:
python3 -m pip install fusor
See the installation instructions in the documentation for a description of dependency setup requirements.
Usage
Fusion and subcomponent constructors are provided through a core FUSOR class:
>>> from fusor import FUSOR
>>> f = FUSOR()
>>> fusion = f.fusion(
... structure=[
... {
... "type": "GeneElement",
... "gene": {
... "type": "Gene",
... "label": "EWSR1",
... "id": "hgnc:3508"
... }
... },
... {
... "type": "UnknownGeneElement"
... }
... ],
... assay={
... "type": "Assay",
... "methodUri": "pmid:33576979",
... "assayId": "obi:OBI_0003094",
... "assayName": "fluorescence in-situ hybridization assay",
... "fusionDetection": "inferred",
... },
... )
>>> fusion.type
<FUSORTypes.ASSAYED_FUSION: 'AssayedFusion'>
See the usage section in the documentation for more features and code examples.
Feedback and contributing
We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.
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