#!/usr/bin/perl  
use strict;  
use warnings;  
use 5.014;  
  
my %cod;    
$cod{1} = "Int";     
$cod{2} = "non";     
$cod{3} = "syn";     
$cod{4} = "stop";     
  
$SIG{'__WARN__'} = sub{die $_[0]};	     
my $file = "Type 9.txt";     
open IN, "<", $file or die "could not open $file $! \n";     
open OUT, ">", "output.txt" or die "could not open output.txt $! \n";    
print OUT "Coordinate	No of Strains	AA Change\n";     
chomp(my @data = <DATA>);   
my ($SNP, $count, $change);    
while(<IN>){    
	if (m/^FT\s+SNP\s+(\d+)/) {     
			$SNP = $1;		     
	}    
	elsif (m/^FT\s+\/note="(.*)"/) {     
			my $line = $1;  
			$count = 0;  
  
			for my $data (@data) {  
				$count += () = $line =~ /$data/g;	  
			}    
			$line =~ m/\((AA \w+->\w+)\)\s*$/;     
        	$change = $1 || "";     
	}    
	elsif (m/^FT\s+\/colour=(\d+)/) {     
		print OUT "$SNP $count $change\n" if $cod{$1} eq "non";  
	}     
}   
  
__DATA__   
4386_7#8_   
4350_7#6_   
4414_1#6_   
6133_2#2_   
4465_5#1_   
4465_5#6_   
6236_1#3_   
4330_8#8_   
4386_6#1_   
4414_5#9_   
4340_5#10_   
4340_6#11_   
4386_6#8_