https://github.com/biocpy/txdb
Access TxDB Annotation objects
https://github.com/biocpy/txdb
genome-annotation genomicranges txdb
Last synced: 22 days ago
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Access TxDB Annotation objects
- Host: GitHub
- URL: https://github.com/biocpy/txdb
- Owner: BiocPy
- License: mit
- Created: 2025-12-12T05:53:51.000Z (about 2 months ago)
- Default Branch: master
- Last Pushed: 2026-01-12T16:30:47.000Z (24 days ago)
- Last Synced: 2026-01-12T21:59:28.590Z (24 days ago)
- Topics: genome-annotation, genomicranges, txdb
- Language: Python
- Homepage: https://biocpy.github.io/txdb/
- Size: 195 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Authors: AUTHORS.md
Awesome Lists containing this project
README
[](https://pypi.org/project/txdb/)
# TxDb
This 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.
## Install
To get started, install the package from [PyPI](https://pypi.org/project/txdb/)
```bash
pip install txdb
```
## Usage
### Using TxDbRegistry
The TxDbRegistry provides easy access to hosted TxDb databases in [AnnotationHub](https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html).
```python
from txdb import TxDbRegistry
# Initialize registry
registry = TxDbRegistry()
# List available databases
print(registry.list_txdb())
# Load a specific database (downloads and caches it automatically)
# Example: hg38 knownGene
txdb = registry.load_db("TxDb.Hsapiens.UCSC.hg38.knownGene")
# Access features
transcripts = txdb.transcripts()
print(transcripts)
```
## OUTPUT
GenomicRanges with 412044 ranges and 3 metadata columns
seqnames ranges strand _tx_id tx_name tx_type
[0] chr1 11121 - 14413 + | 1 ENST00000832824.1 None
[1] chr1 11125 - 14405 + | 2 ENST00000832825.1 None
[2] chr1 11410 - 14413 + | 3 ENST00000832826.1 None
... ... ... | ... ... ...
[412041] chrX_MU273397v1_alt 314193 - 316302 - | 412042 ENST00000710030.1 None
[412042] chrX_MU273397v1_alt 314813 - 315236 - | 412043 ENST00000710216.1 None
[412043] chrX_MU273397v1_alt 324527 - 324923 - | 412044 ENST00000710031.1 None
------
seqinfo(711 sequences): chr1 chr2 chr3 ... chrX_MU273395v1_alt chrX_MU273396v1_alt chrX_MU273397v1_alt
### Using a Local TxDb File
If you have a local SQLite file (e.g., generated from R), you can load it directly.
```python
from txdb import TxDb
txdb = TxDb("path/to/custom_txdb.sqlite")
# Extract exons
exons = txdb.exons()
# Extract promoters (2kb upstream)
promoters = txdb.promoters(upstream=2000, downstream=200)
# Filter for a specific chromosome
chr1_tx = txdb.transcripts(filter={"tx_chrom": "chr1"})
```
Check out the documentation for all supported extractors from TxDB files.
## Note
This project has been set up using [BiocSetup](https://github.com/biocpy/biocsetup)
and [PyScaffold](https://pyscaffold.org/).