use strict;
use warnings;
use feature qw(say);

my $file = "BSAC.pl";
my %cod = ( 1 => "red", 2 => "non", 3 => "green" );
open my $in, "<", "$file";
open my $out, ">", "output.txt";
say $out "Coordinate   No of Strains   AA Change";

my $SNP;
my $count;
my $change;
while ( my $line = <$in> ) {
    chomp $line;
    say qq(DEBUG: Line = "$line");
    if ( $line =~ /^FT\s+SNP\s+(\d+)/ ){
        $SNP = $1;        
        say qq(\$SNP = $1;);
    } 
    elsif ( $line =~ /^FT\s+\/note="(.*)"/) {
        my $note = $1;
        say qq(my \$note = $1);
        $count = ($note =~ tr/=/=/);
        $note =~ /\((AA \w+->\w+)\)\s*$/;
        $change = $1 || "";
    }
    elsif ( $line =~ /^FT\s+\/colour=(\d+)/ ) {
        say qq(Code = $1);
        if ( $cod{$1} eq "non" ) {
            printf $out "%-12.12s %-15.15s %s\n",  $SNP, $count, $change;
        }
    }
}