Shell Programming and Scripting

Gene1 1
Gene1 2
Gene1 3
Gene1 0
Gene2 0
Gene2 0
Gene2 4
Gene2 8
Gene3 9
Gene3 9
Gene4 0

If the first column matches, then look in the second column. If there is a value of zero in the second column, then don't consider that record while averaging.

Gene1 2 (3+2+1/3. Because the fourth value is zero)
Gene2 6
Gene3 9
Gene4 0

sort infile |
        awk '{arr[$1]+=$2; cnt[$1]+=($2>0 )? 1: 0 ; next}
         END (for(i in arr) { printf( "%s  %f\n", i, arr[i]/cnt[i]) } > newfile

awk '{if($2!=0) {print $0}}' input > temp && mv temp input

cat input

Gene1 1
Gene1 2
Gene1 3
Gene2 4
Gene2 8
Gene3 9
Gene3 9

awk '{a[$1]+=$2}END{for (i in a) print i,a[i]}' input

Gene1 6
Gene2 12
Gene3 18

awk '
        {
                A[$1] += $2
                T[$1] += ( $2 == 0 ? 0 : 1 )
        }
        END {
                for ( k in A )
                        print k, ( T[k] ? A[k] / T[k] : 0 )
        }
' file

' file | sort

awk '{a[$1]+=$2; cnt[$1]+=($2==0?0:1)}END{for (i in a) print i,(a[i]?a[i]/cnt[i]:0)}' 1