#!/usr/bin/perl 
use strict;
use warnings;

print "The lower the score the more stable the structure.", "\n",
	  "Please set a limiting value e.g. -3: ", "\n";
my $value = <STDIN>;


open IN, "file.hairpin", or die $!;

my @trash;
my @treasure;

while (<IN>){
	if ($_ =~ /^>+/){
	push @treasure, $_;

	}elsif($_ =~ /^None+/){
	push @trash, $_;

	}elsif($_ =~ /(^d+)/){

## Here	I don't know how to incorporate the value I get from the user with the value
## in the file
		
	}else{
	push @treasure, $_;
	}
}

close IN;

foreach my $stuff (@treasure){
	open SIFTED, '>>', "new_file.hairpin", or die $!;
	print SIFTED, $stuff."\n";
	close SIFTED;
}