I have a file that has numeric values in the form of a matrix. I have written an awk script that prints the header, then adds 1 to the columns 'sum' if the values in the columns are less than 5 and greater than 0. Then, at the end, it prints the sum of each column. This part works fine:
awk ' BEGIN {FS=OFS=" "} NR==1 {print} NR>1 {for (i=1;i<=NF;i++) if ($i < 5 && $i > 0) a[i]+=1} END {for (i=1;i<=NF;i++) printf $a[i]
}' snp_fake2.txt > tmp.txt`My goal is to print the entire column if that columns sum is greater than some value THRESHOLD. I have tried adding an if statement after the second for loop to determine if the columns sum, a[i], is > THRESHOLD, and then printing the column:
awk ' BEGIN {FS=OFS=" "} NR==1 {print} NR>1 {for (i=1;i<=NF;i++) if ($i < 5 && $i > 0) a[i]+=1} END {for (i=1;i<=NF;i++) if (a[i] < THRESHOLD) printf $i
}' snp_fake2.txt > tmp.txt`But when I run this the script does not output the entire column, only a single number. How can I print the entire column instead of just the single value?
12 Answers
AWK processes the file one line at a time. It has no memory of previous lines. The END rule executes after the last line is processed. At this point AWK cannot print all the entries in column $i because it only knows a single value for column $i: the one from the last line.
Your goal requires two passes of the file: one to calculate the column sum, and a second to print out the entire column (for the appropriate columns). To do so, you could write a shell script that calls awk to calculate the sums, and then calls awk (or something else) to print the columns.
0If I understood right, one way is to use two dimensional array. It works with GNU awk.
echo -e '1 4 7\n2 5 8\n3 6 9' | awk '
{ for (i=1;i<=NF;i++) { field[i][NR]=$i if ($i < 5 && $i > 0) { a[i]+=1 } }
}
END { for (i in a) { if (a[i] > 2) { for (j in field[i]) print field[i][j] } }
}'
