This programme is to retrieve potential drug targets (protein, protein complex or RNA molecules) with their correspondinng association scores. The Minimum, Maximum, Average and standard deviation of all associations are also returned.
Assumes you have python 3 installed - https://www.python.org/downloads/
From CMD line -
apt install python-pip
pip install opentargets
Either clone these files from github or just download and save in a folder eg. openTargets
git clone https://github.com/sarahjeeeze/openTargets
cd openTargets
run the tests to check it is set up correctly
python tests.py
Format to run script -
python openTargetsEMBL.py [-t/-d/--help] [searchTerm]
-t Target association search
-d Disease association search
--help Returns doc string
Examples -
python openTargetsEMBL.py -d alpers
python openTargetsEMBL.py -t ENSG00000264781
python openTargetsEMBL.py --help
If input is incorrect you should receive an error message eg.
Disease not found in database, please check input and try again
Incorrect entry must define -t for target or -d for disease
See sampleOutput folder for example of expected output for Kuru disease
Denise Carvalho-Silva, Andrea Pierleoni, Miguel Pignatelli, ChuangKee Ong, Luca Fumis, Nikiforos Karamanis, Miguel Carmona, Adam Faulconbridge, Andrew Hercules, Elaine McAuley, Alfredo Miranda, Gareth Peat, Michaela Spitzer, Jeffrey Barrett, David G Hulcoop, Eliseo Papa, Gautier Koscielny, Ian Dunham, Open Targets Platform: new developments and updates two years on, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1056–D1065, https://doi.org/10.1093/nar/gky1133