Utilities for working with PGS Catalog API and scoring files
Project description
pgscatalog-utils
This convenience package bundles every PGS Catalog application, including:
| Application | Description | Link |
|---|---|---|
pgscatalog-download |
Download scoring files from the PGS Catalog in specific genome builds | README |
pgscatalog-combine |
Combine multiple scoring files into a consistent structure | README |
pgscatalog-relabel |
Relabel values in a column based on values in a column in another file | README |
pgscatalog-match |
Match structured scoring file to variants in target genomes | README |
pgscatalog-matchmerge |
Merge variant match results, useful on larger datasets | README |
pgscatalog-intersect |
Match variants across two different variant information files (e.g. reference & target genomes) | README |
pgscatalog-aggregate |
Aggregate calculated PGS split across multiple files | README |
pgscatalog-ancestry-adjust |
Adjust calculated PGS in the context of genetic ancestry | README |
Please note v1.0.0 contains breaking changes: CLI applications have been renamed and the package has been significantly refactored.
See https://github.com/PGScatalog/pygscatalog for more details.
Installation
or install via pip:
$ pipx install pgscatalog-utils
Documentation
Documentation is available at https://pygscatalog.readthedocs.io/.
Developer instructions
You'll need nox and uv installed.
To get set up with a development environment run:
$ nox -s dev
$ source .venv/bin/activate
This will create a virtual environment in the current directory.
$ pgscatalog-download --help
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file pgscatalog_utils-2.0.0.tar.gz.
File metadata
- Download URL: pgscatalog_utils-2.0.0.tar.gz
- Upload date:
- Size: 3.2 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.12.9
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
1341bbc10c622f4cf3df7f1f472e5d787c8356ccf08ddea9c8b25219f6683387
|
|
| MD5 |
e2451a38df94a8d84346957f35463a59
|
|
| BLAKE2b-256 |
85df2e5c27f43f4e04c3f70e7fe365604a60753e40e5b3edfc74aaad7654bf96
|
Provenance
The following attestation bundles were made for pgscatalog_utils-2.0.0.tar.gz:
Publisher:
publish.yml on PGScatalog/pygscatalog
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
pgscatalog_utils-2.0.0.tar.gz -
Subject digest:
1341bbc10c622f4cf3df7f1f472e5d787c8356ccf08ddea9c8b25219f6683387 - Sigstore transparency entry: 233842275
- Sigstore integration time:
-
Permalink:
PGScatalog/pygscatalog@025912dad98ad756af635d57500fcf3d7dbdeefd -
Branch / Tag:
refs/heads/main - Owner: https://github.com/PGScatalog
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@025912dad98ad756af635d57500fcf3d7dbdeefd -
Trigger Event:
workflow_dispatch
-
Statement type:
File details
Details for the file pgscatalog_utils-2.0.0-py3-none-any.whl.
File metadata
- Download URL: pgscatalog_utils-2.0.0-py3-none-any.whl
- Upload date:
- Size: 6.9 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.12.9
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
e4e761bb0c52db6b63a7b926c26e1a25922ca3d81726b8ce51049a394edf1385
|
|
| MD5 |
b3e35cccf125fe41cdce3932c8b92c88
|
|
| BLAKE2b-256 |
2d2be0e5e38b0664e19e19c0eb92c7707091db574cc303fb0d6bd71c662c7807
|
Provenance
The following attestation bundles were made for pgscatalog_utils-2.0.0-py3-none-any.whl:
Publisher:
publish.yml on PGScatalog/pygscatalog
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
pgscatalog_utils-2.0.0-py3-none-any.whl -
Subject digest:
e4e761bb0c52db6b63a7b926c26e1a25922ca3d81726b8ce51049a394edf1385 - Sigstore transparency entry: 233842282
- Sigstore integration time:
-
Permalink:
PGScatalog/pygscatalog@025912dad98ad756af635d57500fcf3d7dbdeefd -
Branch / Tag:
refs/heads/main - Owner: https://github.com/PGScatalog
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@025912dad98ad756af635d57500fcf3d7dbdeefd -
Trigger Event:
workflow_dispatch
-
Statement type:
