G4RNA Screener development repository provides the code used to train and test G4NN. It contains G4RNA screener's production repository and acts as a wrapper. – README.md

README.md

README

In Progress

USER INFO

Instigator

name: Jean-Michel Garant

email: jean-michel.garant@usherbrooke.ca

gitlab username: J-Michel

REPO INFO

gitlab url: gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener_dev

Version: G4RNA screener development no-tags

This repository provides all the functions needed to build, train and test an ANN comparable to G4NN. We provide it to share the concept since we currently can't provide access to the local psql instance of G4RNA database. We provide this code in case somebody would like to adapt it to its own set of sequences. Feel free to contact the instigator of the project to have more information and support.

This work is an extend of the G4RNA screener and is therefore provided to the public under the same GPL3 license.

DEPENDENCIES

Here are listed dependencies in format:

library_name (recommended version)
From environment
python2.7 (2.7.12)
R (3.2.3)
From Python
biopython (1.68)
mysql-connector-python (2.1.4)
numpy (1.11.0)
pandas (0.18.1)
psycopg2 (2.6.2)
PyBrain (0.3)
regex (2016.9.22)
rpy2 (2.8.3)
scipy (0.18.1)

mysql-connector-python (2.1.4) is not available through pip but here are the steps to follow to install it:

cd PATH/TO/PYTHON/dist-packages/    or    cd PATH/TO/PYTHON/site-packages/
sudo -i
wget https://dev.mysql.com/get/Downloads/Connector-Python/mysql-connector-python-2.1.4.tar.gz
tar -xzf mysql-connector-python-2.1.4.tar.gz
cd mysql-connector-python-2.1.4
python setup.py install
From R
ROCR (1.0-7)

GLOSSARY