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Recent Releases of https://github.com/cancervariants/fusor

https://github.com/cancervariants/fusor -

What's Changed

  • fix!: Remove (::) divider for inferred fusions by @jarbesfeld in https://github.com/cancervariants/fusor/pull/268
  • fix!: Modify fixtures and tests to reduce testing time by @jarbesfeld in https://github.com/cancervariants/fusor/pull/271
  • docs: Ensure documentation is up-to-date by @jarbesfeld in https://github.com/cancervariants/fusor/pull/272
  • style: update ruff and precommit by @jsstevenson in https://github.com/cancervariants/fusor/pull/275
  • feat!: Create separate translator classes by @jarbesfeld in https://github.com/cancervariants/fusor/pull/273
  • fix!: Add offset to genomic breakpoint calculation in civic, check if start and stop are provided given an exon number by @jarbesfeld in https://github.com/cancervariants/fusor/pull/277
  • feat!: Add support for Molecular Oncology Almanac (MOA) by @jarbesfeld in https://github.com/cancervariants/fusor/pull/281
  • feat: Update contig sequence regex by @jarbesfeld in https://github.com/cancervariants/fusor/pull/283
  • fix!: Fix Cicero test fixture and translator test coordinates by @jarbesfeld in https://github.com/cancervariants/fusor/pull/290
  • feat: Enable configurable data location by @jarbesfeld in https://github.com/cancervariants/fusor/pull/291
  • feat: Save cached files to evidence_matching folder by @jarbesfeld in https://github.com/cancervariants/fusor/pull/296

Full Changelog: https://github.com/cancervariants/fusor/compare/0.7.0...0.8.0

- Python
Published by jarbesfeld 8 months ago

https://github.com/cancervariants/fusor - 0.7.0

What's Changed

  • feat!: Add module for fusion matching by @jarbesfeld in https://github.com/cancervariants/fusor/pull/246
  • docs: Update examples in readthedocs by @jarbesfeld in https://github.com/cancervariants/fusor/pull/257
  • feat!: Add translation step to harvester methods by @jarbesfeld in https://github.com/cancervariants/fusor/pull/261
  • fix(test): Add translator instance to fusion matching test by @jarbesfeld in https://github.com/cancervariants/fusor/pull/266
  • feat!: Update nomenclature to allow for gene symbols without identifiers by @jarbesfeld in https://github.com/cancervariants/fusor/pull/265

Full Changelog: https://github.com/cancervariants/fusor/compare/0.6.0...0.7.0

- Python
Published by jarbesfeld 9 months ago

https://github.com/cancervariants/fusor - 0.6.0

What's Changed

  • build: Update CST and gene-normalizer versions by @jarbesfeld in https://github.com/cancervariants/fusor/pull/244
  • fix!: Update EnFusion harvester by @jarbesfeld in https://github.com/cancervariants/fusor/pull/250
  • feat: Add VICC Nomenclature string to each translated fusion event by @jarbesfeld in https://github.com/cancervariants/fusor/pull/248
  • build: Update civicpy version to 5.0 by @jarbesfeld in https://github.com/cancervariants/fusor/pull/252
  • docs: Add new doc files by @jarbesfeld in https://github.com/cancervariants/fusor/pull/254
  • feat!: Add strand to TranscriptSegmentElement output by @jarbesfeld in https://github.com/cancervariants/fusor/pull/263

Full Changelog: https://github.com/cancervariants/fusor/compare/0.5.0...0.6.0

- Python
Published by jarbesfeld 10 months ago

https://github.com/cancervariants/fusor - 0.5.0

What's Changed

  • build: Update cool-seq-tool version by @jarbesfeld in https://github.com/cancervariants/fusor/pull/192
  • feat: Add translator modules for JAFFA and STAR-Fusion fusion detection algorithms by @jarbesfeld in https://github.com/cancervariants/fusor/pull/193
  • docs: fix link typo by @jsstevenson in https://github.com/cancervariants/fusor/pull/195
  • chore: add acceptance criteria to issue templates by @jsstevenson in https://github.com/cancervariants/fusor/pull/199
  • cicd: update precommit configs by @jsstevenson in https://github.com/cancervariants/fusor/pull/198
  • style: update ruff configs by @jsstevenson in https://github.com/cancervariants/fusor/pull/197
  • chore: update gitignore by @jsstevenson in https://github.com/cancervariants/fusor/pull/196
  • feat!: change fusion catcher detection algorithm input parameters by @jarbesfeld in https://github.com/cancervariants/fusor/pull/201
  • test(fix): correct enum usage to resolve ValueError in translator tests by @korikuzma in https://github.com/cancervariants/fusor/pull/202
  • feat!: change arriba fusion detection algorithm input parameters by @jarbesfeld in https://github.com/cancervariants/fusor/pull/204
  • feat!: change CICERO fusion detection algorithm input parameters by @jarbesfeld in https://github.com/cancervariants/fusor/pull/206
  • feat!: change EnFusion fusion detection algorithm input parameters by @jarbesfeld in https://github.com/cancervariants/fusor/pull/208
  • feat!: change Genie fusion detection algorithm input parameters by @jarbesfeld in https://github.com/cancervariants/fusor/pull/210
  • fix!: Remove coordinate correction from fusion catcher translator by @jarbesfeld in https://github.com/cancervariants/fusor/pull/212
  • fix: Add gene symbol check in translator methods by @jarbesfeld in https://github.com/cancervariants/fusor/pull/214
  • build!: require python >= 3.11 by @jarbesfeld in https://github.com/cancervariants/fusor/pull/217
  • build: update CST version and pin ga4gh.vrs version by @jarbesfeld in https://github.com/cancervariants/fusor/pull/216
  • feat: Add new metadata classes for AssayedFusion events by @jarbesfeld in https://github.com/cancervariants/fusor/pull/219
  • feat!: Add support for coordinate type in translators by @jarbesfeld in https://github.com/cancervariants/fusor/pull/221
  • feat: add AnchoredReads and ReadData models by @jarbesfeld in https://github.com/cancervariants/fusor/pull/223
  • feat: Update regex for contig sequence by @jarbesfeld in https://github.com/cancervariants/fusor/pull/226
  • feat!: Incorporate metadata classes into translators by @jarbesfeld in https://github.com/cancervariants/fusor/pull/225
  • feat!: Add pydantic classes for output from fusion callers by @jarbesfeld in https://github.com/cancervariants/fusor/pull/228
  • build: Update cool-seq-tool version by @jarbesfeld in https://github.com/cancervariants/fusor/pull/232
  • feat!: Add methods for extracting data from fusion callers by @jarbesfeld in https://github.com/cancervariants/fusor/pull/230
  • feat!: Add support for UnknownGeneElements by @jarbesfeld in https://github.com/cancervariants/fusor/pull/234
  • build!: Update VRS-Python, gene normalizer, and cool-seq-tool versions by @jarbesfeld in https://github.com/cancervariants/fusor/pull/238
  • feat: Add CIViC to CategoricalFusion object translator by @jarbesfeld in https://github.com/cancervariants/fusor/pull/236
  • feat!: Add support for LinkerElement in Arriba translator by @jarbesfeld in https://github.com/cancervariants/fusor/pull/241

Full Changelog: https://github.com/cancervariants/fusor/compare/0.4.4...0.5.0

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/fusor - 0.4.4

What's Changed

  • build: update cool-seq-tool version by @katiestahl in https://github.com/cancervariants/fusor/pull/189

Full Changelog: https://github.com/cancervariants/fusor/compare/0.4.3...0.4.4

- Python
Published by katiestahl over 1 year ago

https://github.com/cancervariants/fusor - 0.4.3

What's Changed

  • fix: return correct message when validation error occurs by @katiestahl in https://github.com/cancervariants/fusor/pull/188

Full Changelog: https://github.com/cancervariants/fusor/compare/0.4.2...0.4.3

- Python
Published by katiestahl over 1 year ago

https://github.com/cancervariants/fusor - 0.4.2

What's Changed

  • fix: attempting to subscript an object by @katiestahl in https://github.com/cancervariants/fusor/pull/184

Full Changelog: https://github.com/cancervariants/fusor/compare/0.4.1...0.4.2

- Python
Published by katiestahl over 1 year ago

https://github.com/cancervariants/fusor - 0.4.1

  • fix: SequenceLocation start/end for TranscriptSegmentElement by @korikuzma in https://github.com/cancervariants/fusor/pull/172
  • feat: add script to generate examples by @korikuzma in https://github.com/cancervariants/fusor/pull/182

Full Changelog: https://github.com/cancervariants/fusor/compare/0.4.0...0.4.1

- Python
Published by korikuzma over 1 year ago

https://github.com/cancervariants/fusor - 0.4.0

What's Changed

  • feat!: update tx segment with new cool-seq-tool structure changes by @katiestahl in https://github.com/cancervariants/fusor/pull/176

Full Changelog: https://github.com/cancervariants/fusor/compare/0.3.0...0.4.0

- Python
Published by katiestahl over 1 year ago

https://github.com/cancervariants/fusor - 0.3.0

What's Changed

  • fix: use correct version number by @jsstevenson in https://github.com/cancervariants/fusor/pull/173
  • fix!: update structural elements with discriminator by @katiestahl in https://github.com/cancervariants/fusor/pull/174
  • feat: add independent nomenclature method by @jsstevenson in https://github.com/cancervariants/fusor/pull/177
  • feat: add resource check by @jsstevenson in https://github.com/cancervariants/fusor/pull/180
  • docs: add docs by @jsstevenson in https://github.com/cancervariants/fusor/pull/169
  • docs: add additional explanations by @jsstevenson in https://github.com/cancervariants/fusor/pull/181

Full Changelog: https://github.com/cancervariants/fusor/compare/0.2.0...0.3.0

- Python
Published by jsstevenson over 1 year ago

https://github.com/cancervariants/fusor - 0.2.0

What's Changed

  • style: update ruff configs by @jsstevenson in https://github.com/cancervariants/fusor/pull/155
  • build!: use setuptools-scm for version declaration by @jsstevenson in https://github.com/cancervariants/fusor/pull/154
  • cicd: update actions from template by @jsstevenson in https://github.com/cancervariants/fusor/pull/153
  • cicd: update precommit by @jsstevenson in https://github.com/cancervariants/fusor/pull/156
  • chore: add zenodo badge by @jsstevenson in https://github.com/cancervariants/fusor/pull/157
  • build!: update cool-seq-tool version by @katiestahl in https://github.com/cancervariants/fusor/pull/159
  • fix(cicd): add reference to stalebot by @korikuzma in https://github.com/cancervariants/fusor/pull/161
  • feat!: enable cool-seq-tool injection by @jsstevenson in https://github.com/cancervariants/fusor/pull/158
  • cicd: allow missing credentials in aws credentials detection by @jsstevenson in https://github.com/cancervariants/fusor/pull/162
  • docs: update docstring format by @jsstevenson in https://github.com/cancervariants/fusor/pull/164
  • feat!: add reading frame to assayed fusions by @jsstevenson in https://github.com/cancervariants/fusor/pull/163
  • feat!: don't redefine Strand model by @jsstevenson in https://github.com/cancervariants/fusor/pull/168
  • feat!: update to vrs 2.0 models by @katiestahl in https://github.com/cancervariants/fusor/pull/166

Full Changelog: https://github.com/cancervariants/fusor/compare/0.1.0...0.1.1

- Python
Published by jsstevenson over 1 year ago

https://github.com/cancervariants/fusor - 0.1.0

What's Changed

  • cicd: update style checks and test coverage dependencies by @jsstevenson in https://github.com/cancervariants/fusor/pull/121
  • fix: order of ALK fusion by @katiestahl in https://github.com/cancervariants/fusor/pull/120
  • feat: validate multi gene requirement by @jsstevenson in https://github.com/cancervariants/fusor/pull/123
  • fix: catch alternate gene descriptor structure by @jsstevenson in https://github.com/cancervariants/fusor/pull/125
  • feat: relax requirements on minimum information model components to g… by @katiestahl in https://github.com/cancervariants/fusor/pull/129
  • feat: relax requirements on minimum information model by @katiestahl in https://github.com/cancervariants/fusor/pull/131
  • cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/fusor/pull/133
  • build!: upgrade to pydantic v2 by @katiestahl in https://github.com/cancervariants/fusor/pull/135
  • style: use ruff for formatting by @jsstevenson in https://github.com/cancervariants/fusor/pull/138
  • build: use pyproject.toml for build configs by @jsstevenson in https://github.com/cancervariants/fusor/pull/142
  • chore: reorganize internals by @jsstevenson in https://github.com/cancervariants/fusor/pull/140
  • style: pin ruff version to match template by @jsstevenson in https://github.com/cancervariants/fusor/pull/143
  • build: reorganize metadata by @jsstevenson in https://github.com/cancervariants/fusor/pull/144
  • cicd: require priority label for PR by @jsstevenson in https://github.com/cancervariants/fusor/pull/145
  • docs: README glow up by @jsstevenson in https://github.com/cancervariants/fusor/pull/146
  • cicd: remove close issue action by @jsstevenson in https://github.com/cancervariants/fusor/pull/147
  • build: require python >= 3.10 by @jsstevenson in https://github.com/cancervariants/fusor/pull/149

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.27...0.1.0

- Python
Published by katiestahl over 1 year ago

https://github.com/cancervariants/fusor - v0.0.30-dev1

What's Changed

  • feat: relax requirements on minimum information model by @katiestahl in https://github.com/cancervariants/fusor/pull/131

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.28-dev1...v.0.0.30-dev1

- Python
Published by katiestahl over 2 years ago

https://github.com/cancervariants/fusor - v0.0.28-dev1

What's Changed

  • fix: catch alternate gene descriptor structure by @jsstevenson in https://github.com/cancervariants/fusor/pull/125
  • feat: relax requirements on minimum information model components to g… by @katiestahl in https://github.com/cancervariants/fusor/pull/129

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.28-dev0...v0.0.28-dev1

- Python
Published by jsstevenson over 2 years ago

https://github.com/cancervariants/fusor - v0.0.29-dev0

What's Changed

  • fix: catch alternate gene descriptor structure by @jsstevenson in https://github.com/cancervariants/fusor/pull/125
  • feat: relax requirements on minimum information model components to g… by @katiestahl in https://github.com/cancervariants/fusor/pull/129

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.28-dev0...v0.0.29-dev0

- Python
Published by katiestahl over 2 years ago

https://github.com/cancervariants/fusor - v0.0.28-dev0

What's Changed

  • cicd: update style checks and test coverage dependencies by @jsstevenson in https://github.com/cancervariants/fusor/pull/121
  • fix: order of ALK fusion by @katiestahl in https://github.com/cancervariants/fusor/pull/120
  • feat: validate multi gene requirement by @jsstevenson in https://github.com/cancervariants/fusor/pull/123

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.27...v0.0.28-dev0

- Python
Published by jsstevenson over 2 years ago

https://github.com/cancervariants/fusor - v0.0.27

What's Changed

  • fix: remove identifier prefixes from nomenclature by @jsstevenson in https://github.com/cancervariants/fusor/pull/114
  • perf: reuse gene normalizer instance by @jsstevenson in https://github.com/cancervariants/fusor/pull/115
  • chore: update license by @jsstevenson in https://github.com/cancervariants/fusor/pull/116
  • build: update cool-seq-tool dependency by @jsstevenson in https://github.com/cancervariants/fusor/pull/117

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.26...v0.0.27

- Python
Published by jsstevenson over 2 years ago

https://github.com/cancervariants/fusor - v0.0.26

What's Changed

  • build: update dependencies to support latest gene norm release by @jsstevenson in https://github.com/cancervariants/fusor/pull/108
  • build: update dependencies to support latest gene norm release (#108) by @jsstevenson in https://github.com/cancervariants/fusor/pull/110
  • chore: increment version number by @jsstevenson in https://github.com/cancervariants/fusor/pull/111

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.25...v0.0.26

- Python
Published by jsstevenson almost 3 years ago

https://github.com/cancervariants/fusor -

What's Changed

  • updating demo data by @katiestahl in https://github.com/cancervariants/fusor/pull/102

New Contributors

  • @katiestahl made their first contribution in https://github.com/cancervariants/fusor/pull/102

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.24...v0.0.25

- Python
Published by jsstevenson over 3 years ago

https://github.com/cancervariants/fusor - v0.0.24

What's Changed

  • ci: bump action versions by @jsstevenson in https://github.com/cancervariants/fusor/pull/103
  • build!: pin dependency versions + update readme by @korikuzma in https://github.com/cancervariants/fusor/pull/105

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.23...v0.0.24

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/fusor - v0.0.23

What's Changed

  • fix: misc nomenclature bugs by @jsstevenson in https://github.com/cancervariants/fusor/pull/98
  • feat: add inferred nomenclature by @jsstevenson in https://github.com/cancervariants/fusor/pull/99

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.22...v0.0.23

- Python
Published by jsstevenson over 3 years ago

https://github.com/cancervariants/fusor - v0.0.22

What's Changed

  • Build out a few more fusion examples, pulled largely from the fusion docs, and remove the biologically-meaningless ones
  • Make demo data accessible via import
  • Freeze and specify some dependencies to ensure install works
  • Update regulatory element nomenclature and structure per late-June manuscript updates

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.21...v0.0.22

- Python
Published by jsstevenson over 3 years ago

https://github.com/cancervariants/fusor -

  • fix: junction nomenclature to remove additional _

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/fusor - v0.0.20

  • feat: incorporate latest assay attribute updates
  • ci: clean up test configs
  • feat: add model schema example checks

- Python
Published by jsstevenson almost 4 years ago

https://github.com/cancervariants/fusor -

• add latest information model updates • use newest uta-tools release

- Python
Published by jsstevenson almost 4 years ago

https://github.com/cancervariants/fusor - v0.0.18

What's Changed

  • feat: catch up to latest manuscript changes by @jsstevenson in https://github.com/cancervariants/fusor/pull/80
  • ci: add issue close action by @jsstevenson in https://github.com/cancervariants/fusor/pull/81
  • feat: 5/26 information model updates for regulatory element by @jsstevenson in https://github.com/cancervariants/fusor/pull/83
  • release by @jsstevenson in https://github.com/cancervariants/fusor/pull/84

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.17...v0.0.18

- Python
Published by jsstevenson almost 4 years ago

https://github.com/cancervariants/fusor -

  • Add CategoricalFusion and AssayedFusion classes
  • Add AssayedFusion evidence and observation classes
  • Update RegulatoryElement properties
  • Update nomenclature generation

- Python
Published by jsstevenson about 4 years ago

https://github.com/cancervariants/fusor -

  • Fix setup bug

- Python
Published by jsstevenson about 4 years ago

https://github.com/cancervariants/fusor -

  • Add method to generate nomenclature consistent with the fusion specification
  • Add importable version value
  • Sequence ID bugfixes
  • Provide biologically meaningful examples

- Python
Published by jsstevenson about 4 years ago

https://github.com/cancervariants/fusor -

  • Update dependencies

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.13

  • Fix one off position error
  • Change various domain references to "functional_domains" and "FunctionalDomain"
  • Add LocationDescriptor to FunctionalDomain entities

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.12

  • Add regulatory element constructor

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.11

What's Changed

  • Add any_gene component to Fusion by @jsstevenson in https://github.com/cancervariants/fusor/pull/45

Full Changelog: https://github.com/cancervariants/fusor/compare/v0.0.10...v0.0.11

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.10

  • GenomicRegionComponent -> TemplatedSequenceComponent
  • Split TranscriptSegmentComponent.component_genomic_region into TranscriptSegmentComponent.component_genomic_start and TranscriptSegmentComponent.component_genomic_end, each of which should be a single-coordinate LocationDescriptor
  • Exon Start and Exon End can be optional
  • Bring in pipeline related functions from Fusion Curation
  • Use uta_tools for coordinate fetching
  • Add gene normalizer
  • Generate ga4gh digest for sequence_id
  • Add SequenceLocation location_id

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.9

  • add any_gene component
  • add sequence_id to SequenceLocation objects
  • temporarily fix jsonschema dependency issue

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor -

  • Linker sequence accepts the following regex: ^[A-Za-z*\-]*$

- Python
Published by korikuzma over 4 years ago

https://github.com/cancervariants/fusor - v0.0.7

  • misc bugfixes

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.6

  • Update to latest VRS/VRSATILE requirements
  • Import classes from VRS-Pydantic rather than defining them locally

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor - v0.0.5

  • new name
  • significant model changes to better align with VRS, VRSATILE specifications

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/fusor -

  • Model for structuring gene fusions

- Python
Published by korikuzma over 4 years ago