I will keep in mind about the things you mentioned above (sorry about Formatting, this was my first post).

I was trying something like this (just a snippet of my code):

$scafSeq = $ARGV[0];
open (IN, "< $scafSeq");

while ( $line = <IN> ) 
    {
        chomp $line;
        $line =~ s/^\s+//g;
        $line =~ s/sequence/count/g;
        next if $line eq "";

        if(substr($line,0,1) eq ">")
        {
            ($scaff) = $line =~ /^>(\S+)/;
        }
        else
        {
            $scaffData -> {$scaff} .= $line; 
        }
    }
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And then I sort the keys and split it with N. Although this approach was sorting the data for >sequence1, etc , it was not working for >C1113456... data.

Your code is short and effective, to do this job. Thanks!