gencode_mouse_5000.result: gencode_mouse_5000.svm gencode_mouse_5000.predict
	perl /home/yduan/usr/bin/bin/svmresult.pl gencode_mouse_5000.svm gencode_mouse_5000.predict > gencode_mouse_5000.result

gencode_mouse_5000.predict: gencode_mouse_5000.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.model
	/home/yduan/usr/bin/bin/svm-predict -b 1 gencode_mouse_5000.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.model gencode_mouse_5000.predict
gencode_mouse_5000.scaled: gencode_mouse_5000.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 gencode_mouse_5000.svm > gencode_mouse_5000.scaled

gencode_mouse_5000.svm: gencode_mouse_5000.list gencode_mouse_5000.orf gencode_mouse_5000.feature all_gencode_mouse_5000.consv
	perl /home/yduan/usr/bin/bin/merge.pl gencode_mouse_5000.list all_gencode_mouse_5000.consv gencode_mouse_5000.orf gencode_mouse_5000.feature > gencode_mouse_5000.svm

gencode_mouse_5000.gtf: /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/gencode_mouse/wd/gencode_mouse_5000.gtf
	/home/yduan/usr/bin/bin/gffread -o /dev/stdout /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/gencode_mouse/wd/gencode_mouse_5000.gtf | perl -ne 'print unless /^#/' | perl -ne '$$_="chr$$_" unless /^chr/; $$_=~s/Parent=/transcript_id /; print ' > gencode_mouse_5000.gtf

gencode_mouse_5000.fa: gencode_mouse_5000.gtf
	/home/yduan/usr/bin/bin/gffread -g /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/genome/mm10 -w gencode_mouse_5000.fa gencode_mouse_5000.gtf

gencode_mouse_5000.list: gencode_mouse_5000.fa
	perl /home/yduan/usr/bin/bin/fa2list.pl gencode_mouse_5000.fa gencode_mouse_5000.list

gencode_mouse_5000.feature: gencode_mouse_5000.fa
	perl /home/yduan/usr/bin/bin/fa2feature.pl gencode_mouse_5000.fa gencode_mouse_5000.feature

gencode_mouse_5000.orf: gencode_mouse_5000.fa
	/home/yduan/usr/bin/bin/txCdsPredict -anyStart gencode_mouse_5000.fa gencode_mouse_5000.orf

consv/Makefile: gencode_mouse_5000.gtf
	cd consv && perl /home/yduan/usr/bin/bin/prepare_consv.pl ../gencode_mouse_5000.gtf /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/consv/mm10 /home/yduan/usr/bin/bin/calcConsv all_gencode_mouse_5000.consv > Makefile && cd ..

all_gencode_mouse_5000.consv: consv/Makefile
	cd consv && make -j 1 && cd ..

clean:
	rm -rf consv/* *gencode_mouse_5000.*