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https://github.com/danymukesha/ensembl-variant-lookup

Python tool built for a user-friendly interface for searching individual variants, batch queries, and exploring gene regions from the Ensembl database.

https://github.com/danymukesha/ensembl-variant-lookup

Science Score: 13.0%

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    Low similarity (11.5%) to scientific vocabulary

Keywords

api ensembl-rest genomics-data variants
Last synced: 5 months ago · JSON representation

Repository

Python tool built for a user-friendly interface for searching individual variants, batch queries, and exploring gene regions from the Ensembl database.

Basic Info
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
api ensembl-rest genomics-data variants
Created about 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme

README.md

Ensembl Variant Lookup

Ensembl Variant Lookup provides a web-based graphical interface, allowing users to retrieve information about genetic variants based on their Reference SNP ID (RSID). This application integrates with the Ensembl Variant API to provide detailed variant information.

Overview

Ensembl Variant Lookup is a Python tool built with Flask that allows users to query and retrieve information about genetic variants from the Ensembl database. It provides a user-friendly interface for searching individual variants, batch queries, and exploring gene regions. The tool is designed to streamline the retrieval of essential genetic variant data, making it a valuable resource for genomics research and exploration.

Features

  • Single Variant Lookup: Retrieve detailed information about a specific genetic variant using its RSID.
  • Batch Variant Lookup: Perform batch searches by entering a list of RSIDs and obtaining information for multiple variants simultaneously.
  • Gene Lookup: Fetch information about a specific gene, including details on associated variants.

Simplified illustration at high-level of API exposed in thie application, it includes all the API endpoints in the diagram:

mermaid graph TD A[User's Browser] -->|GET /| B[Flask Application] B -->|GET /| C[Render index.html] C -->|Form Submission| D[Flask Application] D -->|POST /batch| E[Render batch_results.html] C -->|Form Submission| F[Flask Application] F -->|POST /visualize| G[Render visualization.html] C -->|Form Submission| H[Flask Application] H -->|POST /variant| I[Render variant_results.html] C -->|GET /gene_region| J[Flask Application] J -->|GET /gene_region| K[Render gene_region_results.html]

This flowchart now includes the following API endpoints:

  • /batch (POST): Batch search for variants by rsid list.
  • /variant (POST): Search for variants by rsid.
  • /gene_region (GET): Search for variants in a gene region.
  • /visualize (POST): Visualize variants for a specific gene.

Installation

Use pip to install the Ensembl Variant Lookup package.

bash pip install ensembl-variant-lookup

Usage

  1. Run the Application:

    bash ensembl-variant-lookup

    This command starts the Flask development server, and you can access the application at http://localhost:5000 in your web browser.

  2. Access the Web Interface:

    Open your web browser and navigate to http://localhost:5000 to use the Ensembl Variant Lookup tool.

  3. Single Variant Lookup:

-   Enter a specific RSID in the provided form.
-   Click the "Fetch Variant" button to retrieve detailed information for the specified genetic variant.
  1. Batch Variant Lookup:
-   Enter a list of RSIDs (comma-separated) in the batch search form.
-   Click the "Batch Search" button to obtain information for multiple variants simultaneously.
  1. Gene Lookup:
-   Enter the gene name in the gene lookup form.
-   Click the "Fetch Gene Info" button to retrieve details about the specified gene.

Screenshots

Home

Caption 1: Screenshot of the Home Page.

Single Variant Lookup

Caption 2: Screenshot of the Single Variant Lookup interface.

Batch Variant Lookup

Caption 3: Screenshot of the Batch Variant Lookup interface.

Gene Lookup

Caption 4: Screenshot of the Gene Lookup interface.

Contributing

If you would like to contribute to this project, please contact or leave here an issue issue

Owner

  • Name: Dany Mukesha
  • Login: danymukesha
  • Kind: user
  • Location: Rome, Italy

GitHub Events

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Last synced: 8 months ago

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  • Total Commits: 24
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Dany Mukesha d****a@F****l 2

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Dependencies

poetry.lock pypi
  • iniconfig 2.0.0 develop
  • packaging 23.2 develop
  • pluggy 1.3.0 develop
  • pytest 7.4.4 develop
  • requests-mock 1.11.0 develop
  • six 1.16.0 develop
  • blinker 1.7.0
  • certifi 2023.11.17
  • charset-normalizer 3.3.2
  • click 8.1.7
  • colorama 0.4.6
  • flask 2.3.3
  • idna 3.6
  • itsdangerous 2.1.2
  • jinja2 3.1.3
  • markupsafe 2.1.3
  • requests 2.31.0
  • urllib3 2.1.0
  • werkzeug 3.0.1
pyproject.toml pypi
  • flask ^2.0
  • python ^3.11
  • requests ^2.26
  • pytest ^7.4.4 test
  • requests-mock ^1.11.0 test
requirements.txt pypi
  • blinker ==1.7.0
  • certifi ==2023.11.17
  • charset-normalizer ==3.3.2
  • click ==8.1.7
  • colorama ==0.4.6
  • flask ==2.3.3
  • idna ==3.6
  • itsdangerous ==2.1.2
  • jinja2 ==3.1.3
  • markupsafe ==2.1.3
  • requests ==2.31.0
  • urllib3 ==2.1.0
  • werkzeug ==3.0.1