merged_no_G_test.result: merged_no_G_test.svm merged_no_G_test.predict
	perl /home/yduan/usr/bin/bin/svmresult.pl merged_no_G_test.svm merged_no_G_test.predict > merged_no_G_test.result

merged_no_G_test.predict: merged_no_G_test.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.model
	/home/yduan/usr/bin/bin/svm-predict -b 1 merged_no_G_test.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.model merged_no_G_test.predict
merged_no_G_test.scaled: merged_no_G_test.svm /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.scale.param
	/home/yduan/usr/bin/bin/svm-scale -r /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.scale.param merged_no_G_test.svm > merged_no_G_test.scaled

merged_no_G_test.svm: merged_no_G_test.list merged_no_G_test.orf merged_no_G_test.feature all_merged_no_G_test.consv
	perl /home/yduan/usr/bin/bin/merge.pl merged_no_G_test.list all_merged_no_G_test.consv merged_no_G_test.orf merged_no_G_test.feature > merged_no_G_test.svm

merged_no_G_test.gtf: /home/yduan/work_file/lncRNAdb/methods_assement/data_for_prediction/random_5k_data/simu/mouse/output/sim100/ass/lncRNAtest/with_out_G/result/wd/merged_no_G_test.gtf
	/home/yduan/usr/bin/bin/gffread -o /dev/stdout /home/yduan/work_file/lncRNAdb/methods_assement/data_for_prediction/random_5k_data/simu/mouse/output/sim100/ass/lncRNAtest/with_out_G/result/wd/merged_no_G_test.gtf | perl -ne 'print unless /^#/' | perl -ne '$$_="chr$$_" unless /^chr/; $$_=~s/Parent=/transcript_id /; print ' > merged_no_G_test.gtf

merged_no_G_test.fa: merged_no_G_test.gtf
	/home/yduan/usr/bin/bin/gffread -g /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/genome/mm10 -w merged_no_G_test.fa merged_no_G_test.gtf

merged_no_G_test.list: merged_no_G_test.fa
	perl /home/yduan/usr/bin/bin/fa2list.pl merged_no_G_test.fa merged_no_G_test.list

merged_no_G_test.feature: merged_no_G_test.fa
	perl /home/yduan/usr/bin/bin/fa2feature.pl merged_no_G_test.fa merged_no_G_test.feature

merged_no_G_test.orf: merged_no_G_test.fa
	/home/yduan/usr/bin/bin/txCdsPredict -anyStart merged_no_G_test.fa merged_no_G_test.orf

consv/Makefile: merged_no_G_test.gtf
	cd consv && perl /home/yduan/usr/bin/bin/prepare_consv.pl ../merged_no_G_test.gtf /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/consv/mm10 /home/yduan/usr/bin/bin/calcConsv all_merged_no_G_test.consv > Makefile && cd ..

all_merged_no_G_test.consv: consv/Makefile
	cd consv && make -j 1 && cd ..

clean:
	rm -rf consv/* *merged_no_G_test.*