refseq_mouse_5000.result: refseq_mouse_5000.svm refseq_mouse_5000.predict
	perl /home/yduan/usr/bin/bin/svmresult.pl refseq_mouse_5000.svm refseq_mouse_5000.predict > refseq_mouse_5000.result

refseq_mouse_5000.predict: refseq_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 refseq_mouse_5000.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/mm10.model refseq_mouse_5000.predict
refseq_mouse_5000.scaled: refseq_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 refseq_mouse_5000.svm > refseq_mouse_5000.scaled

refseq_mouse_5000.svm: refseq_mouse_5000.list refseq_mouse_5000.orf refseq_mouse_5000.feature all_refseq_mouse_5000.consv
	perl /home/yduan/usr/bin/bin/merge.pl refseq_mouse_5000.list all_refseq_mouse_5000.consv refseq_mouse_5000.orf refseq_mouse_5000.feature > refseq_mouse_5000.svm

refseq_mouse_5000.gtf: /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/refseq_mouse/wd/refseq_mouse_5000.gtf
	/home/yduan/usr/bin/bin/gffread -o /dev/stdout /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/refseq_mouse/wd/refseq_mouse_5000.gtf | perl -ne 'print unless /^#/' | perl -ne '$$_="chr$$_" unless /^chr/; $$_=~s/Parent=/transcript_id /; print ' > refseq_mouse_5000.gtf

refseq_mouse_5000.fa: refseq_mouse_5000.gtf
	/home/yduan/usr/bin/bin/gffread -g /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/genome/mm10 -w refseq_mouse_5000.fa refseq_mouse_5000.gtf

refseq_mouse_5000.list: refseq_mouse_5000.fa
	perl /home/yduan/usr/bin/bin/fa2list.pl refseq_mouse_5000.fa refseq_mouse_5000.list

refseq_mouse_5000.feature: refseq_mouse_5000.fa
	perl /home/yduan/usr/bin/bin/fa2feature.pl refseq_mouse_5000.fa refseq_mouse_5000.feature

refseq_mouse_5000.orf: refseq_mouse_5000.fa
	/home/yduan/usr/bin/bin/txCdsPredict -anyStart refseq_mouse_5000.fa refseq_mouse_5000.orf

consv/Makefile: refseq_mouse_5000.gtf
	cd consv && perl /home/yduan/usr/bin/bin/prepare_consv.pl ../refseq_mouse_5000.gtf /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/consv/mm10 /home/yduan/usr/bin/bin/calcConsv all_refseq_mouse_5000.consv > Makefile && cd ..

all_refseq_mouse_5000.consv: consv/Makefile
	cd consv && make -j 1 && cd ..

clean:
	rm -rf consv/* *refseq_mouse_5000.*