# note: this should be run as a single line via the console. Or as is within pycharm.
python /home/john/Documents/workspace/Searchlight2/Searchlight2.py
--out path=/home/john/Documents/workspace/Searchlight2/sample_datasets/results/
--ss file=/home/john/Documents/workspace/Searchlight2/sample_datasets/SS.tsv
--bg file=/home/john/Documents/workspace/Searchlight2/backgrounds/mouse_GRCm38.p6.tsv
--em file=/home/john/Documents/workspace/Searchlight2/sample_datasets/EM.tsv
--ora file=/home/john/Documents/workspace/Searchlight2/gene_set_databases/GO_bp_mouse.tsv,type=GO_BP
--ura file=/home/john/Documents/workspace/Searchlight2/upstream_regulator_databases/trrust.mouse.tsv,type=TRUSST
--de file=/home/john/Documents/workspace/Searchlight2/sample_datasets/WT_vs_KO.tsv,numerator=KO,denominator=WT
--de file=/home/john/Documents/workspace/Searchlight2/sample_datasets/KO_KO_rescue.tsv,numerator=KO_rescue,denominator=KO
--mde name=all,numerator=KO*denominator=WT,numerator=KO_rescue*denominator=KO
