BOL: Count the number of N in fasta file with Perl

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Poonam Mahapatra
Count the number of N in fasta file with Perl

Count the number of N in fasta file with Perl

By Poonam Mahapatra 2668 days ago

#!/usr/bin/perl

my ($h, $n, $l);

open(I,$ARGV[0]) or die($!);
while(<I>){
  chomp;
  if(/^>/){
    $h=substr($_,1);
  }else{
    $n=($_=~tr/nN/nN/);
    $l=length($_);
    print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n";
  }
}
close(I);