VOGDB-API

Introduction

The vDirect is a tool providing various filtering options for the VOGDB-data.

Setting up

Starting a MYSQL Server

Write in terminal

sudo apt-get update
sudo apt-get install mysql-server

set root privileges for the mysql server

sudo mysql
mysql> ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY 'password';
mysql> FLUSH PRIVILEGES;
mysql> exit;

If it worked you should be able to access mysql server as root:

sudo mysql -u root -p
# enter password

Setting up Python environment

python version: 3.8.5

pip install sqlalchemy
pip install sqlalchemy-utils
pip install pymysql
pip install biopython
pip install hypercorn
pip install fastapi

Creating the database

make sure you downloaded the VOGDB data: ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data
put the data folder in the same projects folder

Create the MYSQL database by running generate_db.py script

Note: you may need to change the data path or the MYSQL login credentials

Now you should see the newly created tables in the new MYSQL VOG database:

sudo mysql -u root -p

mysql> show databases;
mysql> use VOGDB;
mysql> show tables;
mysql> describe Protein_profile;

Starting the VOG-API

cd vogfastAPI
hypercorn vogdb:api --reload

Using the VOGDB-API with vDirect

Below is the search hierarchy: first specify vsearch, vsummary or vfetch, then the subsequent parameters.
'-h' provides a list of the parameters that can be used for filtering.

python vdirect.py vsearch     species   species_search_parameters
                              protein   protein_search_parameters
                              vog       vog_search_parameters
                  vsummary    species   species_ids
                              protein   protein_ids
                              vog       vog_ids
                  vfetch      protein   faa   protein_ids
                                        fna   protein_ids
                              vog       hmm   vog_ids
                                        msa   vog_ids

Docker

Dependencies

Authors

Monika Fink*, Nikola Vinko*, Sigi Koizar*

*University of Vienna

rsprit/vogDocker