Calculate mean of each column ignoring missing data with awk

Question

I have a large tab-separated data table with thousands of rows and dozens of columns and it has missing data marked as \"na\". For example,

na  0.93    na  0         


        

Answer 1

A possible solution:

awk -F"\t" '{for(i=1; i <= NF; i++)
                {if($i == $i+0){sum[i]+=$i; denom[i] += 1;}}}
            END{for(i=1; i<= NF; i++){line=line""sum[i]/(denom[i]?denom[i]:1)FS} 
                print line}' inputFile

The output for the given data:

0.973333    0.9825  0   0.7425  0.01    0.7125

Note that the third column contains only "na" and the output is 0. If you want the output to be na, then change the END{...}-block to:

END{for(i=1; i<= NF; i++){line=line""(denom[i] ? sum[i]/denom[i]:"na")FS} print line}'