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": {
                    "primaryCoding": {
    ...                 "id": "hgnc:3508",
                        "code": "HGNC:3508",
                        "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
                    }
                    "conceptType": "Gene",
                    "name": "EWSR1"
...             }
...         },
...         {
...           "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.