README.EXAMPLES

#fit predict
eden/bin/convert.py -i examples/bursi.gspan -f gspan -o bursi -v
eden/bin/fit.py -i bursi/data.nld -y examples/bursi.target -r 2 -d 2 -p none -x -o bursi.model -v 
eden/bin/predict.py -i bursi/data.nld -m bursi.model -o bursi.pred -v 

#fit predict one-class
eden/bin/convert.py -i examples/bursi.pos.gspan -o bursi.pos.dat
eden/bin/fit.py -i bursi.pos.dat/data.nld -1 -f 0.1 -r 3 -d 3 -v -o bursi.pos.model
eden/bin/convert.py -i examples/bursi.neg.gspan -o bursi.neg.dat
eden/bin/predict.py -i bursi.pos.dat/data.nld -m bursi.pos.model -o bursi.pos.predictions -v
eden/bin/predict.py -i bursi.neg.dat/data.nld -m bursi.pos.model -o bursi.neg.predictions -v

#annotate
eden/bin/convert.py -i examples/bursi.gspan -f gspan -o bursi -v
eden/bin/fit.py -i bursi/data.nld -y examples/bursi.target -r 2 -d 2 -p none -x -o bursi_out -v 
eden/bin/annotate.py -i bursi/data.nld -o bursi_out/ -v
eden/bin/fit.py -i bursi_out/annotated.nld -y examples/bursi.target -r 2 -d 2 -p none -x -o bursi_annotated_out -v

#motif
num=1000
dat=DATA/AGO/AGO.right_allUs.seq
cat $dat | unsort 2>/dev/null | head -$num > AGO2
eden/bin/convert.py -i dataset.seq -f sequence -o AGO2_dat -v
eden/bin/fit.py -i AGO2_dat/data.nld -r 7 -d 7 -p none -x -v -y dataset.target -o AGO2_out
eden/bin/convert.py -i AGO2 -f sequence -o AGO2_pos_dat -v
eden/bin/max_subarrays.py -i AGO2_pos_dat/data.nld -v -o AGO2_out/
cat AGO2_out/subarrays  | sort | uniq -c | sort -nr | head -20 | awk '$1>1{print $2}'  | awk '{print ">ID" NR; print $0}' | tee motif.fa

#align
eden/bin/misc/create_motif_artificial_dataset.py -n 2  -k 9 -d 10 -s 80 -r 90
eden/bin/convert.py -i dataset.seq -f sequence -o motif_posneg -v
eden/bin/convert.py -i dataset_positive.seq -f sequence -o motif_pos -v
eden/bin/fit.py -i motif_posneg/data.nld -y dataset.target -r 2 -d 2 -p none -x -o motif_out -v
eden/bin/alignment.py -i motif_pos/data.nld -g -0.1 -r 1.2  -o motif_out 
less motif_out/alignments.txt 


#remote data
for i in $(seq 10 20); do dat=RF002$i; eden/bin/convert.py -t url -i "http://rfam.xfam.org/family/$dat/alignment?acc=$dat&format=fastau&download=0" -f FASTA -o ${dat}_out;  done
eden/bin/fit.py -i RF00210_out/data.nld -n RF00216_out/data.nld -r 2 -d 2 -p none -x