{"id":37082890,"url":"https://github.com/biocpy/txdb","last_synced_at":"2026-01-14T10:01:20.741Z","repository":{"id":328441965,"uuid":"1114948460","full_name":"BiocPy/txdb","owner":"BiocPy","description":"Access TxDB Annotation objects","archived":false,"fork":false,"pushed_at":"2026-01-12T16:30:47.000Z","size":200,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2026-01-12T21:59:28.590Z","etag":null,"topics":["genome-annotation","genomicranges","txdb"],"latest_commit_sha":null,"homepage":"https://biocpy.github.io/txdb/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BiocPy.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-12-12T05:53:51.000Z","updated_at":"2026-01-06T21:30:32.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/BiocPy/txdb","commit_stats":null,"previous_names":["biocpy/txdb"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/BiocPy/txdb","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2Ftxdb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2Ftxdb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2Ftxdb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2Ftxdb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BiocPy","download_url":"https://codeload.github.com/BiocPy/txdb/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2Ftxdb/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28416490,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T08:38:59.149Z","status":"ssl_error","status_checked_at":"2026-01-14T08:38:43.588Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["genome-annotation","genomicranges","txdb"],"created_at":"2026-01-14T10:01:19.763Z","updated_at":"2026-01-14T10:01:20.729Z","avatar_url":"https://github.com/BiocPy.png","language":"Python","readme":"[![PyPI-Server](https://img.shields.io/pypi/v/txdb.svg)](https://pypi.org/project/txdb/)\n![Unit tests](https://github.com/BiocPy/txdb/actions/workflows/run-tests.yml/badge.svg)\n\n# TxDb\n\nThis package provides a Python interface to access and manipulate genome annotations, implemented in the Bioconductor [GenomicFeatures](https://bioconductor.org/packages/GenomicFeatures) package. It allows users to interact with `TxDb` SQLite databases to extract genomic features such as transcripts, exons, CDS, and promoters as [GenomicRanges](https://github.com/biocpy/genomicranges) objects. It also includes a registry system to easily download and cache standard TxDb annotation files.\n\n## Install\n\nTo get started, install the package from [PyPI](https://pypi.org/project/txdb/)\n\n```bash\npip install txdb\n```\n\n## Usage\n\n### Using TxDbRegistry\n\nThe TxDbRegistry provides easy access to hosted TxDb databases in [AnnotationHub](https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html).\n\n```python\nfrom txdb import TxDbRegistry\n\n# Initialize registry\nregistry = TxDbRegistry()\n\n# List available databases\nprint(registry.list_txdb())\n\n# Load a specific database (downloads and caches it automatically)\n# Example: hg38 knownGene\ntxdb = registry.load_db(\"TxDb.Hsapiens.UCSC.hg38.knownGene\")\n\n# Access features\ntranscripts = txdb.transcripts()\nprint(transcripts)\n```\n\n    ## OUTPUT\n    GenomicRanges with 412044 ranges and 3 metadata columns\n                        seqnames          ranges          strand   _tx_id           tx_name tx_type\n                        \u003cstr\u003e       \u003cIRanges\u003e \u003cndarray[int8]\u003e   \u003clist\u003e            \u003clist\u003e  \u003clist\u003e\n        [0]                chr1   11121 - 14413               + |      1 ENST00000832824.1    None\n        [1]                chr1   11125 - 14405               + |      2 ENST00000832825.1    None\n        [2]                chr1   11410 - 14413               + |      3 ENST00000832826.1    None\n                            ...             ...             ... |    ...               ...     ...\n    [412041] chrX_MU273397v1_alt 314193 - 316302               - | 412042 ENST00000710030.1    None\n    [412042] chrX_MU273397v1_alt 314813 - 315236               - | 412043 ENST00000710216.1    None\n    [412043] chrX_MU273397v1_alt 324527 - 324923               - | 412044 ENST00000710031.1    None\n    ------\n    seqinfo(711 sequences): chr1 chr2 chr3 ... chrX_MU273395v1_alt chrX_MU273396v1_alt chrX_MU273397v1_alt\n\n### Using a Local TxDb File\n\nIf you have a local SQLite file (e.g., generated from R), you can load it directly.\n\n```python\nfrom txdb import TxDb\n\ntxdb = TxDb(\"path/to/custom_txdb.sqlite\")\n\n# Extract exons\nexons = txdb.exons()\n\n# Extract promoters (2kb upstream)\npromoters = txdb.promoters(upstream=2000, downstream=200)\n\n# Filter for a specific chromosome\nchr1_tx = txdb.transcripts(filter={\"tx_chrom\": \"chr1\"})\n```\n\nCheck out the documentation for all supported extractors from TxDB files.\n\n\u003c!-- biocsetup-notes --\u003e\n\n## Note\n\nThis project has been set up using [BiocSetup](https://github.com/biocpy/biocsetup)\nand [PyScaffold](https://pyscaffold.org/).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocpy%2Ftxdb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocpy%2Ftxdb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocpy%2Ftxdb/lists"}