GWASStudio: A Tool for Genomic Data Management

alt text

Overview

GWASStudio is a powerful CLI tool designed for efficient storage, retrieval, and querying of genomic summary statistics. It offers a high-performance infrastructure for handling and analyzing large-scale GWAS and QTL datasets, enabling seamless cross-dataset exploration.

Please see the documentation at https://ht-diva.github.io/gwasstudio/

Core Purpose

GWASStudio provides a unified interface across the CDH infrastructure, handling the ingestion, storage, querying and export of genomic data using high-performance technologies.

Key Functionalities

GWASStudio consists of several key functionalities:

1. Data Ingestion

  • Data Ingestion: Imports summary statistics data and its metadata associated.
  • Support for Multiple Storage Options: Works with both local filesystems and cloud storage (S3).

2. Data Querying

  • Flexible Search: Enables searching metadata using template files.

3. Data Export

  • Selective Export: Extracts subsets of data and its metadata associated based on genomic regions, SNPs, or the entire set of data.

Technical Architecture

GWASStudio leverages several advanced technologies:

  1. TileDB Embedded: A high-performance array storage engine that enables efficient storage and retrieval of genomic data.
  2. MongoDB: A flexible, scalable NoSQL database used for storing and querying metadata associated with genomic datasets.
  3. Dask: Provides distributed computing capabilities for processing large datasets.
  4. Python Ecosystem: Built on Python with libraries like Click/Cloup for CLI interfaces, Pandas for data manipulation, and various genomics-specific tools.

Installation

For detailed installation instructions, please refer to the documentation at https://ht-diva.github.io/gwasstudio/

Usage

For detailed instructions on how to use this tool, please refer to the documentation and check the cli_test scripts for a practical guide by examples.

Citation

Example files are derived from:

The variant call format provides efficient and robust storage of GWAS summary statistics. Matthew Lyon, Shea J Andrews, Ben Elsworth, Tom R Gaunt, Gibran Hemani, Edoardo Marcora. bioRxiv 2020.05.29.115824; doi: https://doi.org/10.1101/2020.05.29.115824

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for gmauro from gravatar.com gmauro

Credits

Author: Gianmauro Cuccuru

Requires

Python <3.13, >=3.10

Provides Extra

plot

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

gwasstudio-3.2.2.tar.gz (60.4 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

gwasstudio-3.2.2-py3-none-any.whl (75.0 kB view details)

Uploaded Python 3

File details

Details for the file gwasstudio-3.2.2.tar.gz.

File metadata

  • Download URL: gwasstudio-3.2.2.tar.gz
  • Upload date:
  • Size: 60.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for gwasstudio-3.2.2.tar.gz
Algorithm Hash digest
SHA256 9152170de6cc652c7eece01625f42a5eeb7889b6a7f2aa83639ca581ebd49317
MD5 ef4d94bf1326fd0aa08ef0284fe9dacb
BLAKE2b-256 c4a03aa542290750702cbff868cb23cd9afe9aa9144cbdedb008d38f4b858997

See more details on using hashes here.

Provenance

The following attestation bundles were made for gwasstudio-3.2.2.tar.gz:

Publisher: release.yml on ht-diva/gwasstudio

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file gwasstudio-3.2.2-py3-none-any.whl.

File metadata

  • Download URL: gwasstudio-3.2.2-py3-none-any.whl
  • Upload date:
  • Size: 75.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for gwasstudio-3.2.2-py3-none-any.whl
Algorithm Hash digest
SHA256 e515ee4598626adfff3ae532f13866cef3a8777080c139a538a5fe19975ee11e
MD5 b3cf1d2510ff6931d9020d28dc21bcf0
BLAKE2b-256 97e4b7fe61349a502e6b655f46c6acae46de6d2116d87ac3eee40d0c8cc5ecb7

See more details on using hashes here.

Provenance

The following attestation bundles were made for gwasstudio-3.2.2-py3-none-any.whl:

Publisher: release.yml on ht-diva/gwasstudio

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page