| Name | vrsix JSON |
| Version |
0.0.1
JSON |
| download |
| home_page | None |
| Summary | Tools for indexing GREGoR VCFs |
| upload_time | 2024-11-29 21:35:58 |
| maintainer | None |
| docs_url | None |
| author | James Stevenson |
| requires_python | >=3.10 |
| license | None |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# vrsix: Indexing VRS-Annotated VCFs
Proof of concept for sqlite-based indexing of ANViL-hosted VCFs annotated with VRS IDs and attributes.
From a VCF, ingest a VRS ID and the corresponding VCF-called location (i.e. sufficient inputs for a tabix lookup), and store them in a sqlite database.
```shell
% vrsix load chr1.vcf
```
Given a VRS ID, retrieve VCF-associated data (output format TBD)
```shell
% vrsix fetch-by-id --db-location=sqlite.db dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG
ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,1,783006
```
Or fetch all rows within a coordinate range:
```shell
% vrsix fetch-by-range --db-location=sqlite.db 1 783000 783200
ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,1,783006
ga4gh:VA.MiasxyXMXtOpsZgGelL3c4QgtflCNLHD,1,783006
ga4gh:VA.5cY2k53xdW7WeHw2WG1HA7jl50iH-r9p,1,783175
ga4gh:VA.jHaXepIvlbnapfPtH_62y-Qm81hCrBYn,1,783175
```
## Set up for development
Ensure that a recent version of the [Rust toolchain](https://www.rust-lang.org/tools/install) is available.
Create a virtual environment and install developer dependencies:
```shell
python3 -m virtualenv venv
source venv/bin/activate
python3 -m pip install -e '.[dev,tests]'
```
This installs Python code as editable, but after any changes to Rust code, run ``maturin develop`` to rebuild the Rust binary:
```shell
maturin develop
```
Be sure to install pre-commit hooks:
```shell
pre-commit install
```
Check Python style with `ruff`:
```shell
python3 -m ruff format . && python3 -m ruff check --fix .
```
Use `cargo fmt` to check Rust style (must be run from within the `rust/` subdirectory):
```shell
cd rust/
cargo fmt
```
Run tests with `pytest`:
```shell
pytest
```
Raw data
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