# reads a column file with gene names of interest

file=/home/areverte/SAGE/nih/FINAL2/gxtissue.sol.gz

N=1
MN=`wc $1 | awk '{print $1}'`
while [ $N -lt $MN ]
do
   col1=`head -$N $1 | tail -1 | awk '{print $1}'`
   zcat $file | awk -v col1=$col1 '$1==col1 {print $2, $3}' | sort > vec1
   Np1=`expr $N + 1`
   while [ $Np1 -le $MN ]
   do
      col2=`head -$Np1 $1 | tail -1 | awk '{print $1}'`
      zcat $file | awk -v col2=$col2 '$1==col2 {print $2, $3}' | sort > vec2
      n=`join vec1 vec2 | awk '{print $2, $3}' | corr | awk 'NR==4 {print $3}'`
      r=`join vec1 vec2 | awk '{print $2, $3}' | corr | awk 'NR==5 {print $3}'`
      echo $col1 $N $col2 $Np1 $r $n >> $1_SAGE.out
      Np1=`expr $Np1 + 1`
   done
   N=`expr $N + 1`
done

awk 'NF==4 {$0=$0" 0 0"}; {print $0}' $1_SAGE.out > jj
mv jj $1_SAGE.out

#./any_matrix.pl $1_SAGE.out $1_SAGE.png
# rm j1 $1.temp.in