Sun May 25 07:21:18 EDT 2025


# ----------------------------------------------------------------------------------------------------------------------------------------
# train grammars
#----------------------------------------------------------------------------------------------------------------------------------------
cd ~/src/Mysrc/tornado

#--------------------------------------------------------------------------------------
# train: tRNAs
# data/tRNAs/tRNA1415/tornado/trna1415_annote_1of1
#--------------------------------------------------------------------------------------
cd ~/src/Mysrc/tornado
for train in trna1415_annote_1of1 ; do \
for grm in g5 g5s g6 g6x g6s g6xs RBG RBG_J3J4 ViennaRNAG ContrafoldG ; do \

echo "grammar: $grm" ;\

bin/grm-train --ml \
--margsavefile  notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_marginal.param \
--null          notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_null.param \
--countsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts \
grammars/"$grm".grm \
data/tRNAs/tRNA1415/tornado/"$train".sto \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".param > \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".train ; \

bin/grm-parse --count --preload \
--paramsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".preload.param \
grammars/"$grm".grm \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts ; \

done
done

for train in trna1415_annote_1of1 ; do \
for grm in RBG ; do \

echo "grammar: $grm" ;\

bin/grm-train --ml \
--margsavefile  notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_marginal.param \
--null          notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_null.param \
--countsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts \
grammars/"$grm".grm \
data/tRNAs/tRNA1415/tornado/"$train".sto \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".param > \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".train ; \

bin/grm-parse --count --preload \
--paramsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".preload.param \
grammars/"$grm".grm \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts ; \

done
done



#--------------------------------------------------------------------------------------
# train: TrATrBTrB (standard for CaCoFold)
# data/TORNADO/RNA2011_benchmark/TORNADO_TrATrBTrB.sto
#--------------------------------------------------------------------------------------
cd ~/src/Mysrc/tornado
for train in TORNADO_TrA TORNADO_TrATrB TORNADO_TrATrBTrB ; do \
for grm  in g5 g5s g6 g6x g6s g6xs RBG RBG_J3J4 ViennaRNAG ContrafoldG ; do \

echo "grammar: $grm" ;\

bin/grm-train --ml \
--margsavefile  notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_marginal.param \
--null          notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm"_null.param \
--countsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts \
grammars/"$grm".grm \
data/TORNADO/RNA2011_benchmark//"$train".sto \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".param > \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".train ; \

bin/grm-parse --count --preload \
--paramsavefile notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".preload.param \
grammars/"$grm".grm \
notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts ; \

done
done


----------------------------------------------------------------------------------------------------------------------------------------
save param in preload format ready to import into R-scape src/covgrammars.c
----------------------------------------------------------------------------------------------------------------------------------------
cd ~/src/Mysrc/tornado

bin/grm-parse --count --preload --paramsavefile notebook/05-2025/g5/TORNADO_trna1415_annote_1of2_g5.preload.param      grammars/g5.grm    notebook/05-2025/g5/TORNADO_trna1415_annote_1of2_g5.counts


----------------------------------------------------------------------------------------------------------------------------------------
fold
----------------------------------------------------------------------------------------------------------------------------------------
cd ~/src/Mysrc/tornado

for method cyk mea ; do \
for grm in g5 ; do \
for train in trna1415_annote_1of1 ; do \
for test in  data/tRNAs/tRNA1415/tornado/trna1415_annote_1of2.sto ; do \


    bin/grm-fold --"$method"
    --gpostfile grammars/"$grm".grm grammars/"$grm".grm
    $test
    notebook/05-2025/"$grm"/"$test"_TORNADO_"$train"_"$grm"."$method"
    notebook/05-2025/"$grm"/TORNADO_"$train"_"$grm".counts ;\


    bin/grm-fold --"$method"
    --gpostfile grammars/"$grm".grm grammars/"$grm".grm
    data/tRNAs/tRNA1415/tornado/trna1415_annote_1of2.sto
    notebook/05-2025/"$grm"/trna1415_annote_1of2_TORNADO_TrATrBTrB_annote_1of2_"$grm"."$method"
    notebook/2023-04_train/"$grm"/TORNADO_TrATrBTrB_"$grm".counts ;\
done

bin/grm-fold --mea --gpostfile grammars/g5.grm grammars/g5.grm  data/tRNAs/tRNA1415/tornado/trna1415_annote_1of2.sto notebook/05-2025/g5/trna1415_annote_1of2_TORNADO_trna1415_annote_1of2_g5.mea notebook/05-2025/g5/TORNADO_trna1415_annote_1of2_g5.counts
