put awk command into a separate file - bash

Question

I did make a code and now would like to make a separate file because the code is a bit long to type but I'm having troubles.
This is my code:
awk 'NF && $1!~/^#/ && $1!~/^#/' rmsd.xvg | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}}
END {for (i=2;i<=NF;i++) {
print "\n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)}}' | sort -u
How can this be done?

Answer 1

Create a file named script.awk, and put:
{ for(i=1;i<=NF;i++) {
sum[i] += $i; sumsq[i] += ($i)^2}
}
END {for (i=2;i<=NF;i++) {
print "\n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)
}
}
into it. Then use:
awk 'NF && $1!~/^#/ && $1!~/^#/' rmsd.xvg | awk -f script.awk | sort -u
But there's no need for two separate awk commands. Change the script to:
/^[##]/ { for(i=1;i<=NF;i++) {
sum[i] += $i; sumsq[i] += ($i)^2}
}
END {for (i=2;i<=NF;i++) {
print "\n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)
}
}
Then:
awk -f script.awk rmsd.xvg | sort -u

Answer 2

You can create a shell script as
#!/bin/bash
awk 'NF && $1!~/^#/ && $1!~/^#/' rmsd.xvg | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}}
END {for (i=2;i<=NF;i++) {
print "\n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)}}' | sort -u
Excecute the script as
$ bash fileName

Answer 3

Note that you have two awk commands. However, the first is just a filter and can trivially be combined with the second. The only issue is that instead of using NR in the END action, you'll need to keep count of how many records were acted upon by the first action. The two scripts combined, along with the adjustment for NR, would look like
NF && $1 !~ /^#/ && $1 !~ /^#/ {
for(i=1;i<=NF;i++) {
sum[i] += $i
sumsq[i] += ($i)^2
}
record_count++
}
END {
for (i=2;i<=NF;i++) {
print "\n", sum[i]/record_count, sqrt((sumsq[i]-sum[i]^2/record_count)/record_count)
}
}
I'm assuming that every line has the same number of fields; otherwise, the value of NF in the END action is just the value of NF on the last line, which may or may not have any meaning.
Once the above is saved in something like script.awk, run it with
awk -f script.awk rmsd.xvg | sort -u