folder=$1
merge /data/zhang/makerman/KnownGenes/kgXref.txt.sub.2010 $1/gene_exp.diff | cut -f1,2,6,9,10-20 | awk '{if($3!="NA"){print $0}}' > $1/gene_exp.ann.diff
merge /data/zhang/makerman/KnownGenes/kgXref.txt.sub.2010 $1/isoform_exp.diff | cut -f1,2,6,9,10-20 | awk '{if($3!="NA"){print $0}}' > $1/isoform_exp.ann.diff

head -1  $1/gene_exp.diff > $1/gene_exp.OK.ann.diff
head -1  $1/gene_exp.diff > $1/gene_exp.yes.ann.diff
head -1  $1/gene_exp.diff > $1/gene_exp.no.ann.diff
head -1  $1/isoform_exp.diff > $1/isoform_exp.OK.ann.diff
head -1  $1/isoform_exp.diff > $1/isoform_exp.yes.ann.diff
head -1  $1/isoform_exp.diff > $1/isoform_exp.no.ann.diff


grep -Fw OK $1/gene_exp.ann.diff >>$1/gene_exp.OK.ann.diff
grep -Fw OK $1/gene_exp.ann.diff | grep -Fw yes | grep -Fwv no >>$1/gene_exp.yes.ann.diff
grep -Fw OK $1/gene_exp.ann.diff | grep -Fw no | grep -Fwv yes >>$1/gene_exp.no.ann.diff
grep -Fw OK $1/isoform_exp.ann.diff >>$1/isoform_exp.OK.ann.diff
grep -Fw OK $1/isoform_exp.ann.diff | grep -Fw yes | grep -Fwv no >>$1/isoform_exp.yes.ann.diff
grep -Fw OK $1/isoform_exp.ann.diff | grep -Fw no | grep -Fwv yes >>$1/isoform_exp.no.ann.diff