data_v0.2.23

• Added Ensembl 111

data_v0.2.22

From now on code/data tags/versions are separate, see #64

• New GFFs: RefSeq RS_2023_10, Ensembl VEP110
• #56 - Fix occasional UTA duplicated exons
• #57 - Correctly handle retrieving genomic position and dealing w/indels in GFF (thanks ltnetcase for reporting)
• #60 - Fix for missing protein IDs due to Genbank / GenBank (thanks holtgrewe)
• #64 - Split code/data versions. json.gz are now labelled according to data schema version (thanks holtgrewe)
• #66 - We now store 'Note' field (thanks holtgrewe for suggestion)
• Renamed 'CHM13v2.0' to 'T2T-CHM13v2.0' so it could work with biocommons bioutils

v0.2.21

• #45 - FastaSeqFetcher - fix alignment gaps properly
• #52 - Added transcripts from Ensembl 110 GRCh38 release
• #53 - UTA to cdot transcript start/end conversion issue

v0.2.20

Handle biotypes correctly in Ensembl

v0.2.19

Ensembl GRCh37 Mito transcripts have proper contig name "NC_012920.1" instead of "MT"

v0.2.17

No code changes in loader library, just data generation. Deleted 0.2.16 as that data had contig issue #43

• #42 - Add Ensembl T2T release
• #43 - Fix chrom/contig conversion in JSON data

v0.2.14

[0.2.14] - 2023-03-21

Added

• #39 - Fasta file SeqFetcher implementation
• Add Ensembl 109 GTF

Changed

• #38 - Differing implementation of get_tx_for_region to hgvs one (reported by Manuel Holtgrewe)
• #35 - Tags (ie MANE Select / RefSeq select etc) should be genome build specific
• #34 - Stick to PyHGVS conventions, throw ValueError: transcript is required on missing transcript

v0.2.12

2022-12-08

Added

• #30 - We now store "tag" attributes (eg "MANE Select", "RefSeq Select")
• Switch to using Ensembl GFF3 (so we can get tags out)
• Add Ensembl 108 GFF3

Changed

• Fix for #25 - GeneInfo currently fails for some records
• Fix for #27 - Change URL for missing RefSeq GFFs