mitrans_coding_5000.result: mitrans_coding_5000.svm mitrans_coding_5000.predict
	perl /home/yduan/usr/bin/bin/svmresult.pl mitrans_coding_5000.svm mitrans_coding_5000.predict > mitrans_coding_5000.result

mitrans_coding_5000.predict: mitrans_coding_5000.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/hg19.model
	/home/yduan/usr/bin/bin/svm-predict -b 1 mitrans_coding_5000.scaled /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/hg19.model mitrans_coding_5000.predict
mitrans_coding_5000.scaled: mitrans_coding_5000.svm /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/hg19.scale.param
	/home/yduan/usr/bin/bin/svm-scale -r /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/model/hg19.scale.param mitrans_coding_5000.svm > mitrans_coding_5000.scaled

mitrans_coding_5000.svm: mitrans_coding_5000.list mitrans_coding_5000.orf mitrans_coding_5000.feature all_mitrans_coding_5000.consv
	perl /home/yduan/usr/bin/bin/merge.pl mitrans_coding_5000.list all_mitrans_coding_5000.consv mitrans_coding_5000.orf mitrans_coding_5000.feature > mitrans_coding_5000.svm

mitrans_coding_5000.gtf: /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/mitrans_coding/wd/mitrans_coding_5000.gtf
	/home/yduan/usr/bin/bin/gffread -o /dev/stdout /home/yduan/work_file/lncRNAdb/methods_assement/prediction_results/random5k/mitrans_coding/wd/mitrans_coding_5000.gtf | perl -ne 'print unless /^#/' | perl -ne '$$_="chr$$_" unless /^chr/; $$_=~s/Parent=/transcript_id /; print ' > mitrans_coding_5000.gtf

mitrans_coding_5000.fa: mitrans_coding_5000.gtf
	/home/yduan/usr/bin/bin/gffread -g /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/genome/hg19 -w mitrans_coding_5000.fa mitrans_coding_5000.gtf

mitrans_coding_5000.list: mitrans_coding_5000.fa
	perl /home/yduan/usr/bin/bin/fa2list.pl mitrans_coding_5000.fa mitrans_coding_5000.list

mitrans_coding_5000.feature: mitrans_coding_5000.fa
	perl /home/yduan/usr/bin/bin/fa2feature.pl mitrans_coding_5000.fa mitrans_coding_5000.feature

mitrans_coding_5000.orf: mitrans_coding_5000.fa
	/home/yduan/usr/bin/bin/txCdsPredict -anyStart mitrans_coding_5000.fa mitrans_coding_5000.orf

consv/Makefile: mitrans_coding_5000.gtf
	cd consv && perl /home/yduan/usr/bin/bin/prepare_consv.pl ../mitrans_coding_5000.gtf /home/yduan/soft/bio/seq/RNA_seq/iSeeRNA-1.2.2/consv/hg19 /home/yduan/usr/bin/bin/calcConsv all_mitrans_coding_5000.consv > Makefile && cd ..

all_mitrans_coding_5000.consv: consv/Makefile
	cd consv && make -j 1 && cd ..

clean:
	rm -rf consv/* *mitrans_coding_5000.*