Releases | Open Source Science

cool-seq-tool - 0.14.3

What's Changed

build: require python >= 3.11 by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/417
fix(types): resolve type errors by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/419
chore: add vscode to gitignore by @zealws in https://github.com/GenomicMedLab/cool-seq-tool/pull/420
fix: add mane refseq genomic to check status by @zealws in https://github.com/GenomicMedLab/cool-seq-tool/pull/416

New Contributors

@zealws made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/420

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.14.2...0.14.3

- Python
Published by korikuzma 10 months ago

cool-seq-tool - 0.14.2

What's Changed

test: resolve deprecation warnings by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/413
feat: add back FeatureOverlap class by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/412
build: remove duplicate polars dep by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/414
build: remove unused deps by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/415

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.14.1...0.14.2

- Python
Published by korikuzma 11 months ago

cool-seq-tool - 0.14.1

What's Changed

style: update ruff and precommit by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/409
build: require stable versions of ga4gh.vrs + pydantic by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/410

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.14.0...0.14.1

- Python
Published by korikuzma 11 months ago

cool-seq-tool - 0.14.0

What's Changed

feat!: Remove validategenomicbreakpoint function by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/405
fix!: Edit logic in genomic breakpoint validator in exongenomiccoords.py by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/406
feat!: Add strand in GenomicTxSeg output by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/408

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.13.1...0.14.0

- Python
Published by korikuzma 12 months ago

cool-seq-tool - 0.13.1

What's Changed

cicd: update precommit/add latest configs by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/401
style: update ruff by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/402
build: bump wags-tails to latest version (v0.3.2) by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/403

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.13.0...0.13.1

- Python
Published by korikuzma about 1 year ago

cool-seq-tool - 0.13.0

What's Changed

feat!: update seqrepo and uta version to 20241220 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/400

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.12.0...0.13.0

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.12.0

What's Changed

feat!: getgenomicmane_genes should return mane status by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/398

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.11.0...0.12.0

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.11.0

What's Changed

feat!: Change breakpoint validation function by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/397

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.10.0...0.11.0

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.10.0

What's Changed

fix!: Add support for residue coords + refactor offset calculation by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/384
feat!: add startingassembly as argument when using genomictotxsegment by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/391

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.9.1...0.10.0

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.9.1

What's Changed

fix: resolve TypeError by using property accessor by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/395

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.9.0...0.9.1

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.9.0

What's Changed

chore: remove unused action by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/376
docs: use correct app name + update transcript selection algorithm by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/379
fix!: Add support for checking before/after transcript boundaries by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/381
docs: add doi badge to readme by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/382
fix: Check to see if there is only one exon in a transcript when selecting the adjacent exon by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/386
chore!: rename optional dependency by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/388
build: pin wags-tails to ~= 0.2.2 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/393

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.8.0...0.9.0

- Python
Published by korikuzma over 1 year ago

cool-seq-tool - 0.8.0

What's Changed

Ensure proper gene symbol comparison by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/373
fix!: Expect user to supply valid, case-sensitive HGNC symbol by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/375

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.7.1...0.8.0

- Python
Published by jarbesfeld over 1 year ago

cool-seq-tool - 0.7.1

What's Changed

refactor!: rename ExonCoord to _ExonCoord to indicate internal use by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/357
refactor: reorder classes and methods in exon_genomic_coords module by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/358
refactor: rename is_start kwarg in private methods to is_seg_start by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/359
refactor: rename _get_alt_ac_start_and_end + flatten output by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/360
refactor: remove duplicate genomic_ac check by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/365
Do not require gene when genomic accession and transcript are provided to genomictotx_segment by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/369
fix: make gene optional param for converting genomic coords as long a… by @katiestahl in https://github.com/GenomicMedLab/cool-seq-tool/pull/370

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.7.0...0.7.1

- Python
Published by katiestahl over 1 year ago

cool-seq-tool - 0.7.0

What's Changed

docs: fix source link by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/331
docs: remove VRS schema support section by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/333
refactor: remove unnecessary literal from AnnotationLayer enum by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/349
feat: enable direct import of CST from package root by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/353
docs: link to stable, not latest by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/355
feat!: Return Pydantic models instead of dicts in UtaDatabase by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/334
feat!: rename residue mode to coordinate type by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/337
feat!: rename ExonGenomicCoordsMapper methods by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/338
feat!: remove UtaDatabase.gettxexons + cleanup exon work by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/347
feat!: remove UtaDatabase.gettxexonsgenomiccoords by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/348
refactor: remove optional strand field from genomictotx_segment by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/340
feat!: rename start/end to genomicstart/genomicend in genomic_to_tx_segment by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/343
feat!: remove optional coordinatetype from genomictotxsegment by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/344
feat!: return Pydantic model in getaltacstartor_end by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/350
feat!: return Pydantic model in UtaDatabase.gettxexonalnv_data by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/351
feat!: update ExonGenomicCoordsMapper + UtaDatabase by @korikuzma and @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/352
fix: genomic accession mismatch when getting nearest tx junction by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/356

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.6.0...0.7.0

- Python
Published by korikuzma almost 2 years ago

cool-seq-tool - 0.6.0

What's Changed

chore: remove unused schemas by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/321
feat: make methods in ManeTranscript public by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/326
fix(test): remove fixture decorator from getprioritizedtranscriptsfromgene by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/328
feat!: only return cdna representation in g_to_mane_c by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/322
feat: add option to g_to_grch38 to return a list of MANE gene(s) by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/325

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.5.1...0.6.0

- Python
Published by korikuzma almost 2 years ago

cool-seq-tool - 0.5.1

What's Changed

cicd: update actions and stale settings from template by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/315
cicd: update precommit by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/316
chore: rename optional dependency by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/317
cicd: use GML reusable-stale action by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/318
cicd: allow missing credentials by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/319
fix: correct strand typo by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/324

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.5.0...0.5.1

- Python
Published by jsstevenson almost 2 years ago

cool-seq-tool - 0.5.0

What's Changed

feat!: use setuptools-scm, capture version at package root by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/301
fix: use correct logging setup by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/303
chore!: remove FastAPI by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/304
feat: consistently handle bare and prefixed chromosome numbering by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/305
refactor: use Assembly enum instead of hard coding by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/306
fix: update handling ClientErrors when getting aws secret value by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/308
fix: resolve DataOrientationWarning for pl.DataFrame by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/309
fix: handle input of alt_ac, not just chromosome by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/312
refactor!: move liftover to separate module by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/310
feat: validate all inputs at once by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/314

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.1...0.5.0

- Python
Published by jsstevenson almost 2 years ago

cool-seq-tool - 0.4.1

What's Changed

fix: scope of resp if breakpoint does not occur on an exon by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/274
docs: add badges by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/275
chore: update license by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/276
cicd: test in python 3.12 by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/277
build: update build metadata by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/278
cicd: add priority label check by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/279
docs: add badges to main readme by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/280
docs: fix residue mode illustration rendering by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/281
fix: don't use deprecated columns param by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/291
feat!: change default postgresql port to 5432 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/292
build: require >= python 3.10 by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/295
fix(docs): correct kwarg in docstring example by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/296
feat!: acquire data with wags-tails, overhaul static file handling by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/290
build: pin polars 1.0 by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/294
chore: add issue templates by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/298
cicd: use builtin token by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/299
chore: add stalebot by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/300
style: update ruff configs by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/302

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev3...0.4.1

- Python
Published by jsstevenson almost 2 years ago

cool-seq-tool - 0.4.0-dev3

What's Changed

build: pin ruff to v0.2.0 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/272
feat: Determine adjacent exon for fusions with non-exonic breakpoint by @jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/268

New Contributors

@jarbesfeld made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/268

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev2...0.4.0-dev3

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.4.0-dev2

What's Changed

fix: StrEnum to Enum for python < 3.11 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/258
docs: add generated changelog by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/259
style: add additional ruff checks by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/260
docs: fix readme links to docs by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/262
build: replace pyliftover with agct to improve performance by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/264
fix: package version by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/265

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev1...0.4.0-dev2

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.4.0-dev1

What's Changed

fix: include package data by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/257

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev0...0.4.0-dev1

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.4.0-dev0

What's Changed

feat!: use latest UTA schema as default by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/223
feat!: include cdna and protein represenation when starting from genomic layer by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/228
docs: add documentation by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/222
docs: add documentation links by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/233
build: remove pipenv support by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/236
build: use pyproject.toml for build config by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/234
test: make doctests work by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/240
fix!: return inter-residue positions instead of zero-based positions by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/235
chore: rm pipfile lock references in .gitignore by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/238
fix: polars InvalidOperationError by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/241
style: use ruff for formatting by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/242
refactor: use enum for strand by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/244
tests: resolve warnings by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/247
refactor!: fix class naming by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/249
refactor!: initial work for cleaning up ExonGenomicCoordsMapper by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/252
chore: remove todo's in tests by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/251

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.3.0-dev1...0.4.0-dev0

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.1.14-dev3

fix: return type for FeatureOverlap getgrch38manegenecds_overlap by @korikuzma in 67a241c

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.14-dev2...0.1.14-dev3

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.1.14-dev2

What's Changed

feat: get cds overlap given chromosome, start, + stop by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/217

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.14-dev1...0.1.14-dev2

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.3.0-dev1

What's Changed

build: properly pin pydantic v2 major version by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/215

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.3.0-dev0...0.3.0-dev1

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.3.0-dev0

What's Changed

cicd: update release.yaml (publish python distribution to pypi) by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/197
refactor!: rearrange app architecture by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/196
refactor: use ResidueMode for residue_mode type by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/199
style: use ruff + black by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/200
refactor: use AnnotationLayer enum by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/203
build: replace pandas with polars (#178) by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/205
refactor!: Update TranscriptPriority enum by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/201
feat: make positions optional in gettranscriptsfrom_gene by @katiestahl in https://github.com/GenomicMedLab/cool-seq-tool/pull/210
refactor!: get_gene_mane_data sorted by desc MANE_Status by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/213
build: pin pydantic to v2 major version by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/214
feat!: create method for GRCh38 to MANE protein representation by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/211

New Contributors

@katiestahl made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/210

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.2.0-dev0...0.3.0-dev0

- Python
Published by korikuzma over 2 years ago

cool-seq-tool - 0.2.0-dev0

What's Changed

build: update pydantic to v2 and remove GeneNormalizer class by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/189

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.14-dev1...0.2.0-dev0

- Python
Published by korikuzma almost 3 years ago

cool-seq-tool - v0.1.14-dev1

What's Changed

build: use standard lib urlparse by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/181
chore: clean up some type annotations by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/183
fix: update FASTA header format by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/182

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.14-dev0...v0.1.14-dev1

- Python
Published by jsstevenson almost 3 years ago

cool-seq-tool - v0.1.14-dev0

What's Changed

refactor: update to lastest version of gene-normalizer by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/146
fix: MANE Summary data >= v1.1 updated GRCh38_chr by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/149
fix: MANE Summary data >= v1.1 updated GRCh38_chr by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/153
build: remove reqs.txt files by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/154
merge staging by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/155
fix: ensure stable imports by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/156
fix: MANETranscriptError in getmappedmane_data by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/160
feat: clean up file download behavior and descriptions by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/163
feat!: remove separate UTA password param by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/166
revert: support for LRG sequences by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/175

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.13...v0.1.14-dev0

- Python
Published by jsstevenson almost 3 years ago

cool-seq-tool - 0.1.13

What's Changed

fix: MANE Summary data >= v1.1 updated GRCh38_chr by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/150

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.12...0.1.13

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - 0.1.12

What's Changed

refactor: update to lastest version of gene-normalizer by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/146

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.11...0.1.12

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - 0.1.11

What's Changed

refactor: add back UTADatabase.liftover38to_37 by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/143

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.10...0.1.11

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - 0.1.10

What's Changed

feat: allow user to provide own chain file for pyliftover by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/136
refactor!: SeqRepoAccess extends vrs-python's SeqRepoDataProxy class by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/138
build: update dependencies by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/139
refactor: remove unused instance variables by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/141

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.9...0.1.10

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - v0.1.9

What's Changed

feat: allow user to provide own chain file for pyliftover (#136) by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/137

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.8...v0.1.9

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - v0.1.8

What's Changed

refactor: use FastApi APIRouter by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/127
fix: order by queries by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/126
feat: accept current gene normalizer query handler by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/130
refactor: allow static file paths to be set via env var by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/133

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.7...v0.1.8

- Python
Published by korikuzma about 3 years ago

cool-seq-tool - v0.1.7

What's Changed

fix: IndexError in getprioritizedtranscriptsfrom_gene by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/118
feat: add alignment mapper class by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/122

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.6...v0.1.7

- Python
Published by korikuzma over 3 years ago

cool-seq-tool - v0.1.6

What's Changed

Update TranscriptSelectionPriority.md by @ahwagner in https://github.com/GenomicMedLab/cool-seq-tool/pull/116
Staging by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/119

New Contributors

@ahwagner made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/116

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.5...v0.1.6

- Python
Published by korikuzma over 3 years ago

cool-seq-tool - v0.1.5

What's Changed

feat: add method for getting mane data given chr + pos by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/114

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.4...v0.1.5

- Python
Published by korikuzma over 3 years ago

cool-seq-tool - v0.1.4

What's Changed

ci: bump action versions by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/109
refactor!: rename uta tools to cool seq tool by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/110
Staging by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/111

Full Changelog: https://github.com/GenomicMedLab/cool-seq-tool/compare/v0.1.3...v0.1.4

- Python
Published by korikuzma over 3 years ago

cool-seq-tool - v0.1.3

What's Changed

feat: add FASTA sequence download by @jsstevenson in https://github.com/GenomicMedLab/uta-tools/pull/106
fix: getting correct tx exons by @korikuzma in https://github.com/GenomicMedLab/uta-tools/pull/107

Full Changelog: https://github.com/GenomicMedLab/uta-tools/compare/v0.1.2...v0.1.3

- Python
Published by jsstevenson over 3 years ago

cool-seq-tool -

Update readme
Update db connection

- Python
Published by korikuzma almost 4 years ago

cool-seq-tool - Zenodo anchor

This is the release for initial Zenodo reference

- Python
Published by ahwagner almost 4 years ago

cool-seq-tool -

refactor: getmappedmane_data should have inter-residue as default

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

feat: create fast api service
- https://uta-tools.genomicmedlab.org/uta_tools
build: Add psycopg2-binary to dev packages
fix: genomic to transcript queries for X/Y chromosomes
fix: get longest compatible transcript data
feat: add endpoint for getting mapped mane data
feat: add endpoint for getting mane transcript

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

Sets PGPASSWORD + UTA_DB_URL for prod env
Sets UTA_DB_URL for local env

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

Fixes index error when querying a transcript position that does not exist on an exon

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

Fix bugs in mane transcript

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

Fixes position bug when using getmanetranscript on genomic coordinate

- Python
Published by korikuzma about 4 years ago

cool-seq-tool -

Update tests for new MANE version
Fix some residue / inter-residue bugs

- Python
Published by korikuzma about 4 years ago