Changelog#

0.8.0#

Released on 2024-10-29 - GitHub - PyPI

What's Changed

Full Changelog: 0.7.1...0.8.0

0.7.1#

Released on 2024-09-26 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.7.0...0.7.1

0.7.0#

Released on 2024-08-21 - GitHub - PyPI

What's Changed

  • docs: fix source link by @jsstevenson in #331
  • docs: remove VRS schema support section by @korikuzma in #333
  • refactor: remove unnecessary literal from AnnotationLayer enum by @korikuzma in #349
  • feat: enable direct import of CST from package root by @jsstevenson in #353
  • docs: link to stable, not latest by @jsstevenson in #355
  • feat!: Return Pydantic models instead of dicts in UtaDatabase by @korikuzma in #334
  • feat!: rename residue mode to coordinate type by @korikuzma in #337
  • feat!: rename ExonGenomicCoordsMapper methods by @korikuzma in #338
  • feat!: remove UtaDatabase.get_tx_exons + cleanup exon work by @korikuzma in #347
  • feat!: remove UtaDatabase.get_tx_exons_genomic_coords by @korikuzma in #348
  • refactor: remove optional strand field from genomic_to_tx_segment by @korikuzma in #340
  • feat!: rename start/end to genomic_start/genomic_end in genomic_to_tx_segment by @korikuzma in #343
  • feat!: remove optional coordinate_type from genomic_to_tx_segment by @korikuzma in #344
  • feat!: return Pydantic model in get_alt_ac_start_or_end by @korikuzma in #350
  • feat!: return Pydantic model in UtaDatabase.get_tx_exon_aln_v_data by @korikuzma in #351
  • feat!: update ExonGenomicCoordsMapper + UtaDatabase by @korikuzma and @jarbesfeld in #352
  • fix: genomic accession mismatch when getting nearest tx junction by @korikuzma in #356

Full Changelog: 0.6.0...0.7.0

0.6.0#

Released on 2024-07-25 - GitHub - PyPI

What's Changed

  • chore: remove unused schemas by @korikuzma in #321
  • feat: make methods in ManeTranscript public by @korikuzma in #326
  • fix(test): remove fixture decorator from get_prioritized_transcripts_from_gene by @korikuzma in #328
  • feat!: only return cdna representation in g_to_mane_c by @korikuzma in #322
  • feat: add option to g_to_grch38 to return a list of MANE gene(s) by @korikuzma in #325

Full Changelog: 0.5.1...0.6.0

0.5.1#

Released on 2024-07-23 - GitHub - PyPI

What's Changed

Full Changelog: 0.5.0...0.5.1

0.5.0#

Released on 2024-07-09 - GitHub - PyPI

What's Changed

Full Changelog: 0.4.1...0.5.0

0.4.1#

Released on 2024-07-02 - GitHub - PyPI

What's Changed

Full Changelog: 0.4.0-dev3...0.4.1

0.4.0-dev3#

Released on 2024-03-01 - GitHub - PyPI

What's Changed

New Contributors

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

0.4.0-dev2#

Released on 2024-02-02 - GitHub - PyPI

What's Changed

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

0.4.0-dev1#

Released on 2024-01-10 - GitHub - PyPI

What's Changed

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

0.4.0-dev0#

Released on 2024-01-10 - GitHub - PyPI

What's Changed

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

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

0.3.0-dev0#

Released on 2023-10-20 - GitHub - PyPI

What's Changed

New Contributors

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

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

v0.1.14-dev0#

Released on 2023-07-21 - GitHub - PyPI

What's Changed

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

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

v0.1.8#

Released on 2023-03-22 - GitHub - PyPI

What's Changed

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

v0.1.7#

Released on 2023-03-02 - GitHub - PyPI

What's Changed

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

v0.1.6#

Released on 2023-02-02 - GitHub - PyPI

What's Changed

New Contributors

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

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

v0.1.3#

Released on 2022-10-13 - GitHub - PyPI

What's Changed

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
  • 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