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Merged
jkanche merged 3 commits into from
Jan 6, 2026
Merged

Query annotation hub for populating the TxDB registry. #5

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ba5e224
Query annotation hub for loading registry of txdb objects.
jkanche Jan 6, 2026
ba94106
remove dead code, update changelog
jkanche Jan 6, 2026
2b0bea3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 6, 2026
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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# Changelog

## Version 0.0.1 - 0.0.3
## Version 0.0.1 - 0.0.4

- Initial release of the package with class structure and basic functionality.
- Fixed minor bugs handling existing resources with cache.
- Download and cache Annotation Hub's sqlite metadata file for querying available TxDB objects.
184 changes: 2 additions & 182 deletions src/txdb/_ahub.py
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__copyright__ = "Jayaram Kancherla"
__license__ = "MIT"

TXDB_CONFIG = {
"TxDb.Athaliana.BioMart.plantsmart22": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart22.sqlite",
},
"TxDb.Athaliana.BioMart.plantsmart25": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart25.sqlite",
},
"TxDb.Athaliana.BioMart.plantsmart28": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Athaliana.BioMart.plantsmart28.sqlite",
},
"TxDb.Btaurus.UCSC.bosTau8.refGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Btaurus.UCSC.bosTau8.refGene.sqlite",
},
"TxDb.Celegans.UCSC.ce11.refGene": {
"release_date": "2019-05-01",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Celegans.UCSC.ce11.refGene.sqlite",
},
"TxDb.Celegans.UCSC.ce6.ensGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Celegans.UCSC.ce6.ensGene.sqlite",
},
"TxDb.Cfamiliaris.UCSC.canFam3.refGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Cfamiliaris.UCSC.canFam3.refGene.sqlite",
},
"TxDb.Dmelanogaster.UCSC.dm3.ensGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Dmelanogaster.UCSC.dm3.ensGene.sqlite",
},
"TxDb.Dmelanogaster.UCSC.dm6.ensGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Dmelanogaster.UCSC.dm6.ensGene.sqlite",
},
"TxDb.Drerio.UCSC.danRer10.refGene": {
"release_date": "2019-05-01",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Drerio.UCSC.danRer10.refGene.sqlite",
},
"TxDb.Ggallus.UCSC.galGal4.refGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Ggallus.UCSC.galGal4.refGene.sqlite",
},
"TxDb.Hsapiens.BioMart.igis": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.BioMart.igis.sqlite",
},
"TxDb.Hsapiens.UCSC.hg18.knownGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.UCSC.hg18.knownGene.sqlite",
},
"TxDb.Hsapiens.UCSC.hg19.knownGene": {
"release_date": "2025-10-29",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.22/TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite",
},
"TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts.sqlite",
},
"TxDb.Hsapiens.UCSC.hg38.knownGene": {
"release_date": "2025-10-29",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.22/TxDb.Hsapiens.UCSC.hg38.knownGene.sqlite",
},
"TxDb.Hsapiens.UCSC.hg38.refGene": {
"release_date": "2024-04-02",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.19/TxDb.Hsapiens.UCSC.hg38.refGene.sqlite",
},
"TxDb.Mmulatta.UCSC.rheMac3.refGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Mmulatta.UCSC.rheMac3.refGene.sqlite",
},
"TxDb.Mmulatta.UCSC.rheMac8.refGene": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Mmulatta.UCSC.rheMac8.refGene.sqlite",
},
"TxDb.Mmulatta.UCSC.rheMac10.refGene": {
"release_date": "2021-10-08",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Mmulatta.UCSC.rheMac10.refGene.sqlite",
},
"TxDb.Mmusculus.UCSC.mm10.ensGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite",
},
"TxDb.Mmusculus.UCSC.mm10.knownGene": {
"release_date": "2019-05-01",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite",
},
"TxDb.Mmusculus.UCSC.mm39.refGene": {
"release_date": "2024-04-02",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.19/TxDb.Mmusculus.UCSC.mm39.refGene.sqlite",
},
"TxDb.Mmusculus.UCSC.mm39.knownGene": {
"release_date": "2025-03-11",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.21/TxDb.Mmusculus.UCSC.mm39.knownGene.sqlite",
},
"TxDb.Mmusculus.UCSC.mm9.knownGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite",
},
"TxDb.Ptroglodytes.UCSC.panTro4.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ptroglodytes.UCSC.panTro4.refGene.sqlite",
},
"TxDb.Ptroglodytes.UCSC.panTro5.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ptroglodytes.UCSC.panTro5.refGene.sqlite",
},
"TxDb.Ptroglodytes.UCSC.panTro6.refGene": {
"release_date": "2019-10-29",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.10/TxDb.Ptroglodytes.UCSC.panTro6.refGene.sqlite",
},
"TxDb.Rnorvegicus.BioMart.igis": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Rnorvegicus.BioMart.igis.sqlite",
},
"TxDb.Rnorvegicus.UCSC.rn4.ensGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Rnorvegicus.UCSC.rn4.ensGene.sqlite",
},
"TxDb.Rnorvegicus.UCSC.rn5.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Rnorvegicus.UCSC.rn5.refGene.sqlite",
},
"TxDb.Rnorvegicus.UCSC.rn6.refGene": {
"release_date": "2019-05-01",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Rnorvegicus.UCSC.rn6.refGene.sqlite",
},
"TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq": {
"release_date": "2020-10-20",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.12/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq.sqlite",
},
"TxDb.Rnorvegicus.UCSC.rn7.refGene": {
"release_date": "2022-04-18",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.15/TxDb.Rnorvegicus.UCSC.rn7.refGene.sqlite",
},
"TxDb.Scerevisiae.UCSC.sacCer2.sgdGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene.sqlite",
},
"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene": {
"release_date": "2016-12-22",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.4/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene.sqlite",
},
"TxDb.Sscrofa.UCSC.susScr3.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Sscrofa.UCSC.susScr3.refGene.sqlite",
},
"TxDb.Sscrofa.UCSC.susScr11.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Sscrofa.UCSC.susScr11.refGene.sqlite",
},
"TxDb.Ggallus.UCSC.galGal5.refGene": {
"release_date": "2020-04-27",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.11/TxDb.Ggallus.UCSC.galGal5.refGene.sqlite",
},
"TxDb.Ggallus.UCSC.galGal6.refGene": {
"release_date": "2019-10-29",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.10/TxDb.Ggallus.UCSC.galGal6.refGene.sqlite",
},
"TxDb.Cfamiliaris.UCSC.canFam4.refGene": {
"release_date": "2021-10-08",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Cfamiliaris.UCSC.canFam4.refGene.sqlite",
},
"TxDb.Cfamiliaris.UCSC.canFam5.refGene": {
"release_date": "2021-10-08",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.14/TxDb.Cfamiliaris.UCSC.canFam5.refGene.sqlite",
},
"TxDb.Cfamiliaris.UCSC.canFam6.refGene": {
"release_date": "2023-04-06",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.17/TxDb.Cfamiliaris.UCSC.canFam6.refGene.sqlite",
},
"TxDb.Celegans.UCSC.ce11.ensGene": {
"release_date": "2022-04-18",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.15/TxDb.Celegans.UCSC.ce11.ensGene.sqlite",
},
"TxDb.Drerio.UCSC.danRer11.refGene": {
"release_date": "2019-05-01",
"url": "https://mghp.osn.xsede.org/bir190004-bucket01/AnnotationHub/ucsc/standard/3.9/TxDb.Drerio.UCSC.danRer11.refGene.sqlite",
},
}

AHUB_METADATA_URL = "https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3"
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