../../software/SCITE/scite -i ../../data/CO5/CO5.master_matrix.scite -names ../../data/CO5/CO5.genenames -n 16 -m 178 -r 1 -l 500000 -fd .1 -ad .3 -e .1 -a -seed 225 -o ./CO5 &> CO5.stats.txt
Rscript name_confs.R CO5_ml0.conf.txt ../../data/CO5/CO5.replacement_table.txt ../../data/CO5/CO5.genenames CO5_ml0.conf.names.txt
python replace.py ../../data/CO5/CO5.replacement_table.txt CO5_ml0.gv CO5_ml0.renamed.gv
Rscript placement_with_conf.R --graph CO5_ml0.renamed.gv --likelihoods CO5_ml0.conf.names.txt --output CO5_ml0.renamed.conf.gv --matrix ../../data/CO5/CO5.master_matrix.txt
Rscript clean.R --graph CO5_ml0.renamed.gv --outdot CO5_ml0.renamed.clean.gv --table CO5_ml0.renamed.clean.txt --matrix ../../data/CO5/CO5.master_matrix.txt
dot CO5_ml0.renamed.clean.gv -T png > CO5.png

../../software/SCITE/scite -i ../../data/CO8/CO8.master_matrix.scite -names ../../data/CO8/CO8.genenames -n 36 -m 182 -r 1 -l 500000 -fd .1 -ad .3 -e .1 -a -seed 225 -o ./CO8 &> CO8.stats.txt
Rscript name_confs.R CO8_ml0.conf.txt ../../data/CO8/CO8.replacement_table.txt ../../data/CO8/CO8.genenames CO8_ml0.conf.names.txt
python replace.py ../../data/CO8/CO8.replacement_table.txt CO8_ml0.gv CO8_ml0.renamed.gv
Rscript placement_with_conf.R --graph CO8_ml0.renamed.gv --likelihoods CO8_ml0.conf.names.txt --output CO8_ml0.renamed.conf.gv --matrix ../../data/CO8/CO8.master_matrix.txt
Rscript clean.R --graph CO8_ml0.renamed.gv --outdot CO8_ml0.renamed.clean.gv --table CO8_ml0.renamed.clean.txt --matrix ../../data/CO8/CO8.master_matrix.txt
dot CO8_ml0.renamed.clean.gv -T png > CO8.png
