Sat Apr 22 12:52:47 EDT 2023


Train several typical models:
-----------------------------
cd ~/src/Mysrc/tornado/notebook/2023-04_train
mkdir g6
mkdir g6s
mkdir g6x
mkdir g6sx
mkdir RBG
mkdir RBG_J3
mkdir RBG_J3J4


on benchmark files:
------------------
~/src/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto


cd g6
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_g6.counts ~/src/Mysrc/tornado/grammars/g6.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_g6.param > TORNADO_TrATrBTrB_g6.train
cd ..

cd g6x
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_g6x.counts ~/src/Mysrc/tornado/grammars/g6x.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_g6x.param > TORNADO_TrATrBTrB_g6x.train
cd ..

cd g6s
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_g6s.counts ~/src/Mysrc/tornado/grammars/g6s.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_g6s.param > TORNADO_TrATrBTrB_g6s.train
cd ..

cd g6xs
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_g6xs.counts ~/src/Mysrc/tornado/grammars/g6xs.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_g6xs.param > TORNADO_TrATrBTrB_g6xs.train
cd ..

cd RBG
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_RBG.counts ~/src/Mysrc/tornado/grammars/RBG.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_RBG.param > TORNADO_TrATrBTrB_RBG.train
cd ..

cd RBG_J3
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_RBG_J3.counts ~/src/Mysrc/tornado/grammars/RBG_J3.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_RBG_J3.param > TORNADO_TrATrBTrB_RBG_J3.train
cd ..

cd RBG_J3J4
~/src/Mysrc/tornado/bin/grm-train --ml --margsavefile TORNADO_TrATrBTrB_marginal.param --null TORNADO_TrATrBTrB_null.param --countsavefile TORNADO_TrATrBTrB_RBG_J3J4.counts ~/src/Mysrc/tornado/grammars/RBG_J3J4.grm ~/src/Mysrc/tornado/data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto TORNADO_TrATrBTrB_RBG_J3J4.param > TORNADO_TrATrBTrB_RBG_J3J4.train
cd ..



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cluster
---------------------------------------------------------------------------------

cd ~/src/Mysrc/tornado

sbatch shscripts/run_tornado.sh g6        TrATrBTrB
sbatch shscripts/run_tornado.sh g6s       TrATrBTrB
sbatch shscripts/run_tornado.sh g6x       TrATrBTrB
sbatch shscripts/run_tornado.sh g6xs      TrATrBTrB
sbatch shscripts/run_tornado.sh RBG       TrATrBTrB
sbatch shscripts/run_tornado.sh RBG_J3    TrATrBTrB
sbatch shscripts/run_tornado.sh RBG_J3J4  TrATrBTrB

sbatch shscripts/run_tornado.sh g6        TrA
sbatch shscripts/run_tornado.sh g6s       TrA
sbatch shscripts/run_tornado.sh g6x       TrA
sbatch shscripts/run_tornado.sh g6xs      TrA
sbatch shscripts/run_tornado.sh RBG       TrA
sbatch shscripts/run_tornado.sh RBG_J3    TrA
sbatch shscripts/run_tornado.sh RBG_J3J4  TrA

sbatch shscripts/run_tornado.sh g6        TrB
sbatch shscripts/run_tornado.sh g6s       TrB
sbatch shscripts/run_tornado.sh g6x       TrB
sbatch shscripts/run_tornado.sh g6xs      TrB
sbatch shscripts/run_tornado.sh RBG       TrB
sbatch shscripts/run_tornado.sh RBG_J3    TrB
sbatch shscripts/run_tornado.sh RBG_J3J4  TrB





----------------------------------------------------------------------------------------------------------------------------------------
save param in preload format ready to inmport into R-scape src/covgrammars.c
----------------------------------------------------------------------------------------------------------------------------------------
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/g6/TORNADO_TrATrBTrB_g6.preload.param      grammars/g6.grm    notebook/2023-04_train/g6/TORNADO_TrATrBTrB_g6.counts
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/g6s/TORNADO_TrATrBTrB_g6s.preload.param    grammars/g6s.grm   notebook/2023-04_train/g6s/TORNADO_TrATrBTrB_g6s.counts
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/g6x/TORNADO_TrATrBTrB_g6x.preload.param    grammars/g6x.grm  notebook/2023-04_train/g6x/TORNADO_TrATrBTrB_g6x.counts
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/g6xs/TORNADO_TrATrBTrB_g6xs.preload.param  grammars/g6xs.grm notebook/2023-04_train/g6xs/TORNADO_TrATrBTrB_g6xs.counts


bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/RBG/TORNADO_TrATrBTrB_RBG.preload.param            grammars/RBG.grm      notebook/2023-04_train/RBG/TORNADO_TrATrBTrB_RBG.counts
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/RBG_J3/TORNADO_TrATrBTrB_RBG_J3.preload.param      grammars/RBG_J3.grm   notebook/2023-04_train/RBG_J3/TORNADO_TrATrBTrB_RBG_J3.counts
bin/grm-parse --count --preload --paramsavefile notebook/2023-04_train/RBG_J3J4/TORNADO_TrATrBTrB_RBG_J3J4.preload.param  grammars/RBG_J3J4.grm notebook/2023-04_train/RBG_J3J4/TORNADO_TrATrBTrB_RBG_J3J4.counts

