fusor 0.7.0

Computable object representation and validation for gene fusions

FUSOR

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Documentation · Installation · Usage · API reference

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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.

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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.

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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.