NONCODE class code file

for org in dm celegans chicken cow human mouse tair yeast zebrafish;
do


hgsql -e 'select * from '$org'_gene_class into outfile "/data/tmp/NONCODEv4_GeneClass/'$org'_gene_class"' ncrna ;


hgsql -e 'select * from '$org'_rnaInGene into outfile "/data/tmp/NONCODEv4_GeneClass/'$org'_rnaInGene"' ncrna;


done


tair=ATHG
cow=BTAG
celegans=CELG
dm=DMEG
zebrafish=DREG
chicken=GGAG
human=HSAG
mouse=MMUG
yeast=SCEG




for org in dm celegans chicken cow human mouse tair yeast zebrafish;
do
cat /data/tmp/NONCODEv4_GeneClass/${org}_gene_class | perl -ne '@t = split(/\t/, $_); $nId = "NON'${!org}'". substr("000000", 0, 6 - length($t[0]."")) . $t[0]; print $nId . "\t" . $t[1];' > ${org}.cc


done


for org in dm celegans chicken cow human mouse tair yeast zebrafish;
do


cat ${org}.cc | cat header - > t
mv t ${org}.cc


done


tair=ATHT
cow=BTAT
celegans=CELT
dm=DMET
zebrafish=DRET
chicken=GGAT
human=HSAT
mouse=MMUT
yeast=SCET


for org in dm celegans chicken cow human mouse tair yeast zebrafish;
do


perl /data/tmp/leftJoin.pl ${org}_rnaInGene 2 ${org}_gene_class 1 | perl -ne '@t = split(/\t/, $_); $nId = "NON'${!org}'". substr("000000", 0, 6 - length($t[0]."")) . $t[0]; print $nId . "\t" . $t[3];' > ${org}_rna.cc


cat ${org}_rna.cc | cat header - > t
mv t ${org}_rna.cc


done


for org in dm celegans chicken cow human mouse tair yeast zebrafish;
do


tar cvzf NONCODEv4_${org}_cc.tgz ${org}*.cc


done