vepyr
vepyr (/ˈvaɪpər/) — VEP Yielding Performant Results — is a blazing-fast Rust
reimplementation of Ensembl's Variant Effect
Predictor, exposed as a
Python library. It builds and uses Ensembl VEP caches locally, annotates VCF
input through a native DataFusion engine, and returns results as a
polars.LazyFrame or a VCF with CSQ in the INFO column.
📚 Documentation
https://biodatageeks.org/vepyr/
| Quick start | Install, get a cache, annotate |
| Download Ensembl VEP and plugin caches | Prebuilt release-116 caches |
| Caches | Cache types, entity schemas, CSQ output fields |
| Plugins | CADD, SpliceAI, AlphaMissense, ClinVar, dbNSFP |
| API reference | build_cache(), annotate(), … |
| Performance | Benchmarks vs Ensembl VEP |
Install
pip install vepyr
See Developers for building from source and running the test suite.
License
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file vepyr-0.5.0.tar.gz.
File metadata
- Download URL: vepyr-0.5.0.tar.gz
- Upload date:
- Size: 4.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
1afe1824512e211f084e298fc86fa964e9516bcc87086ea02dde4a045237d538
|
|
| MD5 |
37cfe76d64d41e3876f3d6c1ae969e30
|
|
| BLAKE2b-256 |
1b17f357c2d9e4a821db6a9336c8784730faa14628b79ae4c95cc87187926a0d
|
Provenance
The following attestation bundles were made for vepyr-0.5.0.tar.gz:
Publisher:
publish_to_pypi.yml on biodatageeks/vepyr
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
vepyr-0.5.0.tar.gz -
Subject digest:
1afe1824512e211f084e298fc86fa964e9516bcc87086ea02dde4a045237d538 - Sigstore transparency entry: 2742282495
- Sigstore integration time:
-
Permalink:
biodatageeks/vepyr@594dd645d839058544d897ee8df1c99c02f12ef1 -
Branch / Tag:
refs/heads/master - Owner: https://github.com/biodatageeks
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_to_pypi.yml@594dd645d839058544d897ee8df1c99c02f12ef1 -
Trigger Event:
workflow_dispatch
-
Statement type:
File details
Details for the file vepyr-0.5.0-cp310-abi3-win_amd64.whl.
File metadata
- Download URL: vepyr-0.5.0-cp310-abi3-win_amd64.whl
- Upload date:
- Size: 53.5 MB
- Tags: CPython 3.10+, Windows x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
c3796ccb06c0740b7592e2ead0286ad2d57501ecde3028facc6d8aac20b44a5b
|
|
| MD5 |
e3712bd0ab6761bc157a3aa98e3fcfea
|
|
| BLAKE2b-256 |
d3536eb3b4d5f7311bf25acecd2557b7f1dd47da160f482471fd5989c060ffea
|
Provenance
The following attestation bundles were made for vepyr-0.5.0-cp310-abi3-win_amd64.whl:
Publisher:
publish_to_pypi.yml on biodatageeks/vepyr
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
vepyr-0.5.0-cp310-abi3-win_amd64.whl -
Subject digest:
c3796ccb06c0740b7592e2ead0286ad2d57501ecde3028facc6d8aac20b44a5b - Sigstore transparency entry: 2742282626
- Sigstore integration time:
-
Permalink:
biodatageeks/vepyr@594dd645d839058544d897ee8df1c99c02f12ef1 -
Branch / Tag:
refs/heads/master - Owner: https://github.com/biodatageeks
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_to_pypi.yml@594dd645d839058544d897ee8df1c99c02f12ef1 -
Trigger Event:
workflow_dispatch
-
Statement type:
File details
Details for the file vepyr-0.5.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.
File metadata
- Download URL: vepyr-0.5.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
- Upload date:
- Size: 60.5 MB
- Tags: CPython 3.10+, manylinux: glibc 2.17+ x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
58a23bccbae912b2ece817fdfb9e7835977e13ab184e80975d7cbcc657b6280e
|
|
| MD5 |
076a1dc1994feab09a6203f5fe85b1f5
|
|
| BLAKE2b-256 |
9286037d9b236a13459ceb591181be44d115b8224e6cb70277ee5d45ea0642f6
|
Provenance
The following attestation bundles were made for vepyr-0.5.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl:
Publisher:
publish_to_pypi.yml on biodatageeks/vepyr
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
vepyr-0.5.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -
Subject digest:
58a23bccbae912b2ece817fdfb9e7835977e13ab184e80975d7cbcc657b6280e - Sigstore transparency entry: 2742282662
- Sigstore integration time:
-
Permalink:
biodatageeks/vepyr@594dd645d839058544d897ee8df1c99c02f12ef1 -
Branch / Tag:
refs/heads/master - Owner: https://github.com/biodatageeks
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_to_pypi.yml@594dd645d839058544d897ee8df1c99c02f12ef1 -
Trigger Event:
workflow_dispatch
-
Statement type:
File details
Details for the file vepyr-0.5.0-cp310-abi3-macosx_11_0_arm64.whl.
File metadata
- Download URL: vepyr-0.5.0-cp310-abi3-macosx_11_0_arm64.whl
- Upload date:
- Size: 54.2 MB
- Tags: CPython 3.10+, macOS 11.0+ ARM64
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
a6bf23b2acc9715132bc7f02458589dfb7835ec6ec4c17fd8669bb4d020afd4b
|
|
| MD5 |
2f846690477bf735e4c8bd3ef9b4d3c7
|
|
| BLAKE2b-256 |
6da533efaee0e028a1f09aecb3b32d1a15b9866a7b2074e809021e04cc4a3b54
|
Provenance
The following attestation bundles were made for vepyr-0.5.0-cp310-abi3-macosx_11_0_arm64.whl:
Publisher:
publish_to_pypi.yml on biodatageeks/vepyr
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
vepyr-0.5.0-cp310-abi3-macosx_11_0_arm64.whl -
Subject digest:
a6bf23b2acc9715132bc7f02458589dfb7835ec6ec4c17fd8669bb4d020afd4b - Sigstore transparency entry: 2742282588
- Sigstore integration time:
-
Permalink:
biodatageeks/vepyr@594dd645d839058544d897ee8df1c99c02f12ef1 -
Branch / Tag:
refs/heads/master - Owner: https://github.com/biodatageeks
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_to_pypi.yml@594dd645d839058544d897ee8df1c99c02f12ef1 -
Trigger Event:
workflow_dispatch
-
Statement type:
File details
Details for the file vepyr-0.5.0-cp310-abi3-macosx_10_12_x86_64.whl.
File metadata
- Download URL: vepyr-0.5.0-cp310-abi3-macosx_10_12_x86_64.whl
- Upload date:
- Size: 57.0 MB
- Tags: CPython 3.10+, macOS 10.12+ x86-64
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
888a57581b877c2a310a81665d5a1a594b3c3ec14d18ed17a59bacb45db5d1d0
|
|
| MD5 |
bef3a210bf9a1fbc36680219ef7a0934
|
|
| BLAKE2b-256 |
8313565f4129ee9293e298aa99a683ca7fd98f80a4705691efa46b1d04acee6c
|
Provenance
The following attestation bundles were made for vepyr-0.5.0-cp310-abi3-macosx_10_12_x86_64.whl:
Publisher:
publish_to_pypi.yml on biodatageeks/vepyr
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
vepyr-0.5.0-cp310-abi3-macosx_10_12_x86_64.whl -
Subject digest:
888a57581b877c2a310a81665d5a1a594b3c3ec14d18ed17a59bacb45db5d1d0 - Sigstore transparency entry: 2742282538
- Sigstore integration time:
-
Permalink:
biodatageeks/vepyr@594dd645d839058544d897ee8df1c99c02f12ef1 -
Branch / Tag:
refs/heads/master - Owner: https://github.com/biodatageeks
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish_to_pypi.yml@594dd645d839058544d897ee8df1c99c02f12ef1 -
Trigger Event:
workflow_dispatch
-
Statement type:
