genome_prepare/script/Pathway.sh

[ $# != 3 ] && echo -e "Usage:\n\t$0 KEGG.txt hsa Pathway.txt" && exit 1
kegg_file=$1
org=$2
outfile=$3
database_dir=/Business/psn_company/Work/Transcriptome/Datum/Public/Database/genome_prepare/KEGG

if [ -s "$database_dir/pathway/$org" ]
then
    sed "s/^$org/map/;s/^map/map/" $database_dir/pathway/$org | sed 's/ - [^-]\+$//' | \
    awk 'BEGIN{FS=OFS="\t"}FNR==NR{a[$1]=$0}FNR!=NR{if(a[$1])print $2,a[$1]}' - $database_dir/pathwayTOKO |sed 's/\tmap/\tko/'|\
    sort -k1,1 -V |awk -F"\t" '{a[$1]=$2"("$3");"a[$1]}END{for(i in a)print i"\t"a[i]}' OFS="\t"| sort -k1,1|sed 's/;$//g' |\
    awk 'BEGIN{FS=OFS="\t"}FNR==NR{a[$1]=$2}FNR!=NR{if(a[$2])print $1,a[$2]}' - $kegg_file > $outfile
else
    echo "Error:$database_dir/pathway/$org not exists"
    exit 1
fi