gg=$1
th=`expr $2`

echo "Gene " $gg "Threshold " $th

echo $gg > lll

awk -v gg=$gg -v th=$th '$1==gg && substr($2,1,2)!="RP" && \
     sqrt($3**2)>th {print $0}' Gene_Corr8_Symb.out | \
sort -n +2 | awk '{print $0}' > ttt1

th=`awk '{print sqrt($3**2)}' ttt1 | sort -n | \
    tail -1 | awk '{print $1}'`

R=1
MR=5
while [ $R -le $MR ]
do
   echo $R $th
   N=1
   MN=`wc ttt1 | awk '{print $1}'`
   while [ $N -le $MN ]
   do
      gg=`head -$N ttt1 | tail -1 | awk '{print $2}'`
      echo $gg
      echo $gg >> lll
      awk -v gg=$gg -v th=$th '$1==gg && substr($2,1,2)!="RP" && \
        sqrt($3**2)>th {print $0}' Gene_Corr8_Symb.out | \
      sort -n +2 | awk '{print $0}' >> ttt2
      N=`expr $N + 1`
   done
   
   th=`awk '{print sqrt($3**2)}' ttt2 | sort -n | \
       tail -1 | awk '{print $1}'`

   awk '{print $2, $2}' ttt2 | sort -u > ttt1
   rm ttt2

   R=`expr $R + 1`
done

gg=$1
echo $gg > $1.list
awk -v gg=$gg '$1!=gg {print $1}' lll | sort -u >> $1.list

rm ttt1 ttt2 lll


awk '{print $1, NR}' $1.list | sort > j1

sort Gene_Corr8_Symb.out | join j1 - | \
awk '{print $3, $0}' | sort | join j1 - | \
awk '{print $3, $4, $1, $2, $6}' | sort -n +1 -n +3 | \
awk '$2<$4 {print $0}' | awk -f pick_largest.awk > $1.temp.in

echo $gg > $1.list
awk -v gg=$gg '$1==gg {print $0}' $1.temp.in | sort -n +4 | \
awk '{print $3}' >> $1.list

rm j1 $1.temp.in

sh mk_ANY_matrix.awk $1.list