#get fasta
gffread -T merged_no_G.gtf -g /home/yduan/work_file/lncRNAdb/methods_assement/data_for_prediction/random_5k_data/simu/mouse/input/templateGenome/mm10Chr.fasta -w merged_no_G.fasta
gffread -T merged_with_G.gtf -g /home/yduan/work_file/lncRNAdb/methods_assement/data_for_prediction/random_5k_data/simu/mouse/input/templateGenome/mm10Chr.fasta -w merged_with_G.fasta
#prepare for lncRNA identification
transeq merged_no_G.fasta merged_no_G.pf.fasta -frame F
transeq merged_with_G.fasta merged_with_G.pf.fasta -frame F
#prepare gtf
cat merged_no_G.gtf | awk '$3!~/transcript/{print}'| grep -v "#" > merged_no_G_test.gtf
cat merged_with_G.gtf | awk '$3!~/transcript/{print}'| grep -v "#" > merged_with_G_test.gtf
#prepare test
mkdir lncRNAtest
cd lncRNAtest/
mkdir with_G
mkdir with_out_G
cd with_G
ln -s ../../merged_with_G.fasta merged.fasta
ln -s ../../merged_with_G.pf.fasta merged.pf.fasta
ln -s ../../merged_with_G_test.gtf merged.gtf
cd ../with_out_G/
ln -s ../../merged_no_G.fasta merged.fasta
ln -s ../../merged_no_G.pf.fasta merged.pf.fasta
ln -s ../../merged_no_G_test.gtf merged.gtf
cd ../../

#prediction
cd lncRNAtest/with_G
/home/yduan/work_file/lncRNAdb/methods_assement/predict_fa.sh merged.fasta result
/home/yduan/work_file/lncRNAdb/methods_assement/predict_gtf.sh merged.fasta merged.gtf mouse result
cd ../with_out_G/
/home/yduan/work_file/lncRNAdb/methods_assement/predict_fa.sh merged.fasta result
/home/yduan/work_file/lncRNAdb/methods_assement/predict_gtf.sh merged.fasta merged.gtf mouse result
cd ../../

#sh patch_cmd