Dear all,

I have one problem, it is only one condition for my easy script for counting of GC content per row

    awk 'NR>1{n=length($1); gc=gsub("[gcGC]", "", $1); print gc/n}' $i

How to count length of row without N character.

for example:

    Input:  ACAGCTTGCNNNN   => length= 9   Gc content=5/9

format of output is not important, only how to count it.

Thanks a lot
Normalized GC content per row sans N

    awk '{gsub("N","");t=length();gsub(/[GC]/,"");print int((t-length())/t*100)/100}'

or, assumes sequence symbols are strictly ACTGN.

    awk '{gsub("N","");t=length();gsub(/[AT]/,"");print int(length()/t*100)/100}'