COMMERCIAL SUPPLIERS
SEQUENCE             /toxin_start="19-94"
                     /translation="MKFFLMCLIIFPIMGVLGKKNGYPL                     CWGACYCFGLEDDKPIGPMKDITKKYCDVQIIPS"
AA ALIGNMENT
full-length{%scorpProtein}, sodium-family{%scorpNA}, putative-group1{%Nag01}, putative-group1c{%Nag01c}
ORIGIN      
   1 acaaaataaa gtgaacttct gaaatcagca cgataaaaag aaacgaaaat gaaatttttc
//
COMMERCIAL SUPPLIERS
SEQUENCE             /toxin_start="19-94"
                     /fragment_start="?"
                     CWGACYCFGLEDDKPIGPMKDITKKYCDVQIIPS"
AA ALIGNMENT
full-length{%scorpProtein}, sodium-family{%scorpNA}, putative-group1{%Nag01}, putative-group1c{%Nag01c}
ORIGIN      
        1 aaaataaagt gaacttctga aatcagcacg ataaaaagaa acgaaaatga aatttttctt
       61 aatgtgtctt atcatcttcc caattatggg agtgcttggc aaaaagaacg gatatcctct
//                         

##</code><code>##

I compile the prog using: perl prog.pl input.db result

#!/usr/bin/perl

my $input = $ARGV[0];
my $output = ">" . $ARGV[1];
my $counter=1;

open(INPUT, $input) or die "Can't open $input.";
open(OUTPUT, $output) or die "Can't open $output.";

$/="\/\/\n";

# Use shorthand for reading file.
while (<>) {
    print OUTPUT $_;
    print $counter;
    $counter++;
}
print "Success\n";
close (INPUT);
close (OUTPUT); 

##</code><code>##

>
while(<INPUT>)