vrsix: Indexing VRS-Annotated VCFs
Overview
vrsix provides a file-based indexing strategy to support fast lookup of AnVIL-hosted VCFs using IDs and annotations drawn from the GA4GH Variation Representation Specification.
See the vrsix Terra workflow for a readymade Terra implementation.
Usage
To get started, you will need a fully VRS-annotated VCF. Confirm that your VCF contains the following info fields:
- VRS_Allele_IDs
- VRS_Starts
- VRS_Stops
- VRS_States
For example, confirm that chr1.vcf has the required fields.
bcftools view -h chr1.vcf | grep '^##INFO='
From a VRSified 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.
vrsix load chr1.vcf
Each variation is stored with an associated file URI to support later retrieval. By default, this URI is simply the input VCF's location in the file system, but you may declare a custom URI instead as an optional argument:
vrsix load chr1.vcf gs://my_stuff/chr1.vcf
By default, all records are ingested into a sqlite file located at ~/.local/share/vrsix.db. This can be overridden with either the environment variable VRS_VCF_INDEX, or with an optional flag to the CLI:
vrsix load --db-location=./vrsix.db input.vcf
Development
Ensure that a recent version of the Rust toolchain is available.
Create a virtual environment and install developer dependencies:
python3 -m venv 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:
maturin develop
Be sure to install pre-commit hooks:
pre-commit install
Check Python style with ruff:
python3 -m ruff format . && python3 -m ruff check --fix .
Use cargo fmt to check Rust style (must be run from within the rust/ subdirectory):
cd rust/
cargo fmt
Run tests from the project root with pytest:
pytest
Some granular tests are written directly into the Rust backend as well:
cd rust/
cargo test
3 maintainers
Release files for vrsix 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| vrsix-0.2.0.tar.gz | 26.0 kB | Details |
Built distributions (wheels)
Total release size: 68.2 MB
Release files / vrsix-0.2.0.tar.gz
| Download URL | vrsix-0.2.0.tar.gz |
|---|---|
| Size | 26.0 kB |
| Tags | Source |
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maturin/1.8.3
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Release files / vrsix-0.2.0-cp313-cp313t-musllinux_1_2_x86_64.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ x86-64 |
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Release files / vrsix-0.2.0-cp313-cp313t-musllinux_1_2_i686.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-musllinux_1_2_i686.whl |
|---|---|
| Size | 3.1 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ x86-32 |
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Release files / vrsix-0.2.0-cp313-cp313t-musllinux_1_2_armv7l.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-musllinux_1_2_armv7l.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ ARMv7l |
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Release files / vrsix-0.2.0-cp313-cp313t-musllinux_1_2_aarch64.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ ARM64 |
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Release files / vrsix-0.2.0-cp313-cp313t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ x86-64 |
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Release files / vrsix-0.2.0-cp313-cp313t-manylinux_2_17_s390x.manylinux2014_s390x.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_s390x.manylinux2014_s390x.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ IBM System/390x |
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| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ PowerPC 64-le |
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| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_i686.manylinux2014_i686.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ x86-32 |
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| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
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| Size | 2.6 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARMv7l |
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| Download URL | vrsix-0.2.0-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 2.7 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARM64 |
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Release files / vrsix-0.2.0-cp313-cp313t-macosx_11_0_arm64.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-macosx_11_0_arm64.whl |
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| Size | 2.5 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading macOS 11.0+ ARM64 |
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Release files / vrsix-0.2.0-cp313-cp313t-macosx_10_12_x86_64.whl
| Download URL | vrsix-0.2.0-cp313-cp313t-macosx_10_12_x86_64.whl |
|---|---|
| Size | 2.6 MB |
| Tags | CPython 3.13 CPython 3.13 free-threading macOS 10.12+ x86-64 |
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Release files / vrsix-0.2.0-cp310-abi3-musllinux_1_2_x86_64.whl
| Download URL | vrsix-0.2.0-cp310-abi3-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 3.0 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-musllinux_1_2_i686.whl |
|---|---|
| Size | 3.1 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-32 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-musllinux_1_2_armv7l.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARMv7l abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-musllinux_1_2_aarch64.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARM64 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl |
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| Size | 3.0 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ IBM System/390x abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ PowerPC 64-le abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_i686.manylinux2014_i686.whl |
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| Size | 2.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-32 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl |
|---|---|
| Size | 2.6 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARMv7l abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Size | 2.7 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 abi3 |
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| Download URL | vrsix-0.2.0-cp310-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 2.5 MB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
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| Download URL | vrsix-0.2.0-cp310-abi3-macosx_10_12_x86_64.whl |
|---|---|
| Size | 2.6 MB |
| Tags | CPython 3.10 abi3 macOS 10.12+ x86-64 |
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