Example of script to query BioMart, parse and create a BridgeDb database
Switch branches/tags
Nothing to show
Clone or download
Pull request Compare This branch is even with JonathanMELIUS:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
lib
src
BioMart2BridgeDb.jar
README.md

README.md

BioMartScript

Introduction

A script to create a BrigdeDb database from BioMart queries.

Run

In your terminal:

java -jar BioMart2BridgeDb.jar <configFile> <outputPath> <oldDB> <inclusive>

  • <configFile>: location of configuration file

  • <outputPath>: Path for the new database

  • <oldDB>: (optional) directory of the old database - run QC

  • <inclusive>: (optional) use inclusive BridgeDb list

List of default config files:

https://github.com/JonathanMELIUS/BioMartScript/tree/bc62ed7fba16dd143292ee10fb4e261d196dd7a6/src/resource

Example: Danio rerio config file

How to create your own config file