Changelog#

0.4.0-dev3#

Released on 2024-03-01 - GitHub - PyPI

What's Changed

build: pin ruff to v0.2.0 by @korikuzma in #272
feat: Determine adjacent exon for fusions with non-exonic breakpoint by @jarbesfeld in #268

New Contributors

@jarbesfeld made their first contribution in #268

Full Changelog: 0.4.0-dev2...0.4.0-dev3

0.4.0-dev2#

Released on 2024-02-02 - GitHub - PyPI

What's Changed

fix: StrEnum to Enum for python < 3.11 by @korikuzma in #258
docs: add generated changelog by @jsstevenson in #259
style: add additional ruff checks by @jsstevenson in #260
docs: fix readme links to docs by @jsstevenson in #262
build: replace pyliftover with agct to improve performance by @korikuzma in #264
fix: package version by @korikuzma in #265

Full Changelog: 0.4.0-dev1...0.4.0-dev2

0.4.0-dev1#

Released on 2024-01-10 - GitHub - PyPI

What's Changed

fix: include package data by @korikuzma in #257

Full Changelog: 0.4.0-dev0...0.4.0-dev1

0.4.0-dev0#

Released on 2024-01-10 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.3.0-dev1...0.4.0-dev0

0.1.14-dev3#

Released on 2023-11-07 - GitHub - PyPI

fix: return type for FeatureOverlap get_grch38_mane_gene_cds_overlap by @korikuzma in 67a241c

Full Changelog: 0.1.14-dev2...0.1.14-dev3

0.1.14-dev2#

Released on 2023-11-07 - GitHub - PyPI

What's Changed

feat: get cds overlap given chromosome, start, + stop by @korikuzma in #217

Full Changelog: v0.1.14-dev1...0.1.14-dev2

0.3.0-dev1#

Released on 2023-10-20 - GitHub - PyPI

What's Changed

build: properly pin pydantic v2 major version by @korikuzma in #215

Full Changelog: 0.3.0-dev0...0.3.0-dev1

0.3.0-dev0#

Released on 2023-10-20 - GitHub - PyPI

What's Changed

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

New Contributors

@katiestahl made their first contribution in #210

Full Changelog: 0.2.0-dev0...0.3.0-dev0

0.2.0-dev0#

Released on 2023-09-11 - GitHub - PyPI

What's Changed

build: update pydantic to v2 and remove GeneNormalizer class by @korikuzma in #189

Full Changelog: v0.1.14-dev1...0.2.0-dev0

v0.1.14-dev1#

Released on 2023-08-21 - GitHub - PyPI

What's Changed

build: use standard lib urlparse by @jsstevenson in #181
chore: clean up some type annotations by @jsstevenson in #183
fix: update FASTA header format by @jsstevenson in #182

Full Changelog: v0.1.14-dev0...v0.1.14-dev1

v0.1.14-dev0#

Released on 2023-07-21 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.1.13...v0.1.14-dev0

0.1.13#

Released on 2023-05-01 - GitHub - PyPI

What's Changed

fix: MANE Summary data >= v1.1 updated GRCh38_chr by @korikuzma in #150

Full Changelog: 0.1.12...0.1.13

0.1.12#

Released on 2023-04-19 - GitHub - PyPI

What's Changed

refactor: update to lastest version of gene-normalizer by @korikuzma in #146

Full Changelog: 0.1.11...0.1.12

0.1.11#

Released on 2023-04-04 - GitHub - PyPI

What's Changed

refactor: add back UTADatabase.liftover_38_to_37 by @korikuzma in #143

Full Changelog: 0.1.10...0.1.11

0.1.10#

Released on 2023-04-04 - GitHub - PyPI

What's Changed

feat: allow user to provide own chain file for pyliftover by @korikuzma in #136
refactor!: SeqRepoAccess extends vrs-python's SeqRepoDataProxy class by @korikuzma in #138
build: update dependencies by @korikuzma in #139
refactor: remove unused instance variables by @korikuzma in #141

Full Changelog: v0.1.9...0.1.10

v0.1.9#

Released on 2023-03-24 - GitHub - PyPI

What's Changed

feat: allow user to provide own chain file for pyliftover (#136) by @korikuzma in #137

Full Changelog: v0.1.8...v0.1.9

v0.1.8#

Released on 2023-03-22 - GitHub - PyPI

What's Changed

refactor: use FastApi APIRouter by @korikuzma in #127
fix: order by queries by @korikuzma in #126
feat: accept current gene normalizer query handler by @korikuzma in #130
refactor: allow static file paths to be set via env var by @korikuzma in #133

Full Changelog: v0.1.7...v0.1.8

v0.1.7#

Released on 2023-03-02 - GitHub - PyPI

What's Changed

fix: IndexError in _get_prioritized_transcripts_from_gene by @korikuzma in #118
feat: add alignment mapper class by @korikuzma in #122

Full Changelog: v0.1.6...v0.1.7

v0.1.6#

Released on 2023-02-02 - GitHub - PyPI

What's Changed

Update TranscriptSelectionPriority.md by @ahwagner in #116
Staging by @korikuzma in #119

New Contributors

@ahwagner made their first contribution in #116

Full Changelog: v0.1.5...v0.1.6

v0.1.5#

Released on 2023-01-05 - GitHub - PyPI

What's Changed

feat: add method for getting mane data given chr + pos by @korikuzma in #114

Full Changelog: v0.1.4...v0.1.5

v0.1.4#

Released on 2022-11-08 - GitHub - PyPI

What's Changed

ci: bump action versions by @jsstevenson in #109
refactor!: rename uta tools to cool seq tool by @korikuzma in #110
Staging by @korikuzma in #111

Full Changelog: v0.1.3...v0.1.4

v0.1.3#

Released on 2022-10-13 - GitHub - PyPI

What's Changed

feat: add FASTA sequence download by @jsstevenson in #106
fix: getting correct tx exons by @korikuzma in #107

Full Changelog: v0.1.2...v0.1.3

v0.1.2: #

Released on 2022-08-10 - GitHub - PyPI

Update readme
Update db connection

zenodo: Zenodo anchor#

Released on 2022-08-10 - GitHub - PyPI

This is the release for initial Zenodo reference

v0.1.1: #

Released on 2022-06-08 - GitHub - PyPI

refactor: get_mapped_mane_data should have inter-residue as default

v0.1.0: #

Released on 2022-06-01 - GitHub - PyPI

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

v0.0.17: #

Released on 2022-05-22 - GitHub - PyPI

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

v0.0.16: #

Released on 2022-04-14 - GitHub - PyPI

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

v0.0.15: #

Released on 2022-04-01 - GitHub - PyPI

Fix bugs in mane transcript

v0.0.14: #

Released on 2022-03-21 - GitHub - PyPI

Fixes position bug when using get_mane_transcript on genomic coordinate

v0.0.13: #

Released on 2022-03-21 - GitHub - PyPI

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

v0.0.12: #

Released on 2021-12-06 - GitHub - PyPI

MANE Transcript data returns inter-residue coordinates
Add flake8-quotes, flake8-annotations, import-order
Move over remaining methods from variation-normalizer
- chromosome <-> accessions, get transcripts given a genomic position + accession, get mane transcript data from a list of transcripts
get_tx_exon_aln_v returns a List

v0.0.10#

Released on 2021-11-17 - GitHub - PyPI

Refactor SeqRepoAcess class
Provide specific, informative feedback upon failure in SeqRepoAccess

v0.0.9: #

Released on 2021-11-09 - GitHub - PyPI

Fix bug when creating connection args to local db
Fix MANE Transcript position bug by adding strand logic

v0.0.8: #

Released on 2021-11-04 - GitHub - PyPI

Add gene to error message in get_alt_ac_start_or_end
Add error checks for MANE transcript genomic data retrieval
Clean up connection to UTA db
Create a new connection pool during execute_query when InvalidAuthorizationSpecificationError is raised

v0.0.7: #

Released on 2021-11-02 - GitHub - PyPI

Fixes more type hints

v0.0.6: #

Released on 2021-11-02 - GitHub - PyPI

Fix 'type' object is not subscriptable in uta_database.py

v0.0.5: #

Released on 2021-11-01 - GitHub - PyPI

Fix bug when getting genomic data for mane transcript when strand is not provided
UTA_TOOLS_PROD -> UTA_DB_PROD env var name change

v0.0.4: #

Released on 2021-10-13 - GitHub - PyPI

Add strand to GenomicDataResponse and TranscriptExonDataResponse

v0.0.3: #

Released on 2021-10-11 - GitHub - PyPI

Add genomic --> transcript exon data
Provide warnings field in response for transcript exon data <-> genomic coordinates
No longer assume exon information for start and end if not provided

v0.0.2: #

Released on 2021-10-04 - GitHub - PyPI

Add UTA queries and MANE Transcript work