Introduction

This project is for rebuiding gene.iobio database based on gene.model.db

Since the gff files are massive, it will take a while to process and read into the database. That said, there is space to optimize. For example, use Dask to process data parallelly.

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Instruction

1. Install

git clone https://github.com/iobio/geneinfo.db.git
cd your project directory

2. Create your virtualenv

python3 -m venv myenv source myenv/bin/activate

3. Install packages and dependencies

pip3 install -r requirements.txt

4. Run

Python3 data_downloader.py
Python3 database_builder.py

5. The new SQLite gene.iobio.db should be deployed in the iobio gru backend

6. Create a new genes.json which is used in the gene.iobio search type-ahead

python3 create_genes.json
cp genes.json ../gene.iobio/client/data/