############pipeline.removeDup##################
#输入参数：org, 比如hg19
#结果文件：newVersionGene.combined.gtf: lncRNA基因文件
#结果文件：${org}.tcons.nc.cnci:非编码的cnci值
#结果文件：${org}.tcons.coding.cnci:编码的cnci值
org=$1;
#分离coding，和noncoding
awk '$4~/NR/{print $0;}' ${org}.refseq.bed > ${org}.refseq.nr.bed
awk '$4~/NM/{print $0;}' ${org}.refseq.bed > ${org}.refseq.nm.bed
perl /leofs/noncode/NONCODEv4/cmds/dup.pl ${org}.refseq.nm.bed 3 > ${org}.refseq.nm.bed.withDup
bedToGtf.sh ${org}.refseq.nm.bed.withDup > ${org}.refseq.nm.gtf
perl /leofs/noncode/NONCODEv4/cmds/dup.pl ${org}.refseq.nr.bed 3 > ${org}.refseq.nr.bed.withDup
bedToGtf.sh ${org}.refseq.nr.bed.withDup > ${org}.refseq.nr.gtf
#分离ENSEMBL中的coding，此处codnig为有对应蛋白产物的转录本
awk -F "," '$3{print $2;}' ensemblProtein > enst.coding
awk -F "," '{print $2;}' ensemblProtein > enst.all
sub.pl enst.coding enst.all > enst.nc
perl /leofs/noncode/NONCODEv4/cmds/leftJoin.pl enst.nc 1 ${org}.ensembl.bed 4 | cut -f 2,3,4,5,6,7,8,9,10,11,12,13 | awk '$1' > ${org}.ensembl.nc.bed
perl /leofs/noncode/NONCODEv4/cmds/leftJoin.pl enst.coding 1 ${org}.ensembl.bed 4 | cut -f 2,3,4,5,6,7,8,9,10,11,12,13| awk '$1' > ${org}.ensembl.coding.bed
perl /leofs/noncode/NONCODEv4/cmds/dup.pl ${org}.ensembl.coding.bed 3 > ${org}.ensembl.coding.bed.withDup
bedToGtf.sh ${org}.ensembl.coding.bed.withDup > ${org}.ensembl.coding.gtf
perl /leofs/noncode/NONCODEv4/cmds/dup.pl ${org}.ensembl.nc.bed 3 > ${org}.ensembl.nc.bed.withDup
bedToGtf.sh ${org}.ensembl.nc.bed.withDup > ${org}.ensembl.nc.gtf
bedToGtf.sh v3.fa.blat.bed > v3.gtf
#合并v3, refseq, ensembl
cuffcompare -r v3.gtf -o mydata -C ${org}.refseq.nr.gtf ${org}.ensembl.nc.gtf v3.gtf
cuffcompare -r ${org}.ensembl.coding.gtf -o mydataVsEnsCoding mydata.combined.gtf -C
awk '$4 == "="{print $5;}' mydataVsEnsCoding.tracking | perl -ne '$_ =~ /q1:.*?\|(.*?)\|/; print $1."\n";' > tcons.maybeCoding.ensembl
cuffcompare -r ${org}.refseq.nm.gtf -o mydataVsRefCoding mydata.combined.gtf -C
awk '$4 == "="{print $5;}' mydataVsRefCoding.tracking | perl -ne '$_ =~ /q1:.*?\|(.*?)\|/; print $1."\n";' > tcons.maybeCoding.refSeq
cat tcons.maybeCoding.ensembl tcons.maybeCoding.refSeq | sort | uniq > tcons.maybeCoding
perl /leofs/noncode/NONCODEv4/cmds/gtfSub.pl tcons.maybeCoding mydata.combined.gtf > newVersion_rmCoding.gtf
gtf2Bed.pl newVersion_rmCoding.gtf > newVersion_rmCoding.bed
#Get the sequence
twoBitToFa -bed=newVersion_rmCoding.bed ${org}.2bit newVersion_rmCoding.fa
perl -ne 'chomp $_; if(/>/){ if($. > 1){ print "\n"; } print $_."\n";}else{ print $_;}' newVersion_rmCoding.fa > newVersion_rmCoding_seqIn1line.fa
#Enter CNCI dir
base=`pwd`
cd cnci
ln -s $base/newVersion_rmCoding_seqIn1line.fa ${org}.fa
perl CNCI.pl -f ${org}.fa -p 20 -l libsvm-3.0 -o ${org} -b
grep noncoding ${org}/cnci.result.file | cut -f 1,3 | sed -e 's/>//' | sed -e 's/score: //' > ../${org}.tcons.nc.cnci
grep coding ${org}/cnci.result.file | cut -f 1,3 | sed -e 's/>//' | sed -e 's/score: //' > ../${org}.tcons.coding.cnci
cd ..
# Leave out of cnci dir
perl $CMD/leftJoin.pl ${org}.tcons.nc.cnci 1 newVersion_rmCoding.bed 4 | cut -f 3,4,5,6,7,8,9,10,11,12,13,14 > newVersion_rmCoding_cnci.bed
getBedSeqLength.sh newVersion_rmCoding_cnci.bed | awk '$2>200' | perl $CMD/leftJoin.pl - 1 newVersion_rmCoding_cnci.bed 4 | cut -f 3,4,5,6,7,8,9,10,11,12,13,14 > newVersion_rmCoding_cnci_lnc.bed
bedToGtf.sh newVersion_rmCoding_cnci_lnc.bed > newVersion_lnc.gtf
cuffcompare -C -o newVersionGene newVersion_lnc.gtf
