this should do exactly what you want. i cleaned up your code a little, and added my comments with ##. you can look up info in perldoc on the items in parentheses. in particular, you may want to look at shift, FileHandle, perlre, split, and while.

some nodes you might want to read are:
while or foreach?
Opening files
Use strict warnings and diagnostics or die
Death to Dot Star!

best of luck in the future!

#!/usr/local/bin/perl -w
use strict;        ## use strict, use strict, use strict!!!
$|++;              ## enable line buffering to STDOUT

use FileHandle; 

# A program that accept an input file: Scorpion database from Gen Bank
# and will output the database in BioWare format

## used descriptive variable names
## used shift operator to process arguments (shift) and die with usage
my $infile = shift || die "usage: $0 infile outfile\n";
my $outfile = shift || die "usage: $0 infile outfile\n";
my $item_count=1;
my $item='D000001';
my $IN = new FileHandle;
my $OUT = new FileHandle;

## check status of open and print $! for descriptive error message
open($IN, "< " . $infile) or die "Can't open $infile. $!";
open($OUT, "> " . $outfile) or die "Can't open $outfile. $!";

while(<$IN>) {
    ## remove trailing newline
    chomp;
    ## skip blank lines
    next if( '^\s*$' );
    ## print newline if end of record
    if( '^//$' ) { print $OUT "\n"; next; }

    ## expects date format like 1or2-three-four characters (perlre)
    if( /^DATE\s+(..?)-(...)-(....)$/ ) { ## very fast regex
        print $OUT "DBACC\t", $item++, "\n";
        print $OUT "DATE\t\"$1-$2 $3\"\n";
    } 
    ## non-greedy match between double quotes (perlre)
    elsif( /^\s*\/exon="(.*?)"$/ ) { 
        ## handle null case
        print $OUT "Exon\t{Translation -}\n" unless $1;
        ## seperate the matched string and process each (split)
        for(split ';', $1) {
            print $OUT "Exon\t{Translation\%", $_ ,"}\n";
        }
    }
    ## non-greedy match between double quotes (perlre)
    elsif( /^\s*\/intron="(.*?)"$/ ) {
        ## handle null case
        print $OUT "Intron\t{Translation -}\n" unless $1;
        ## seperate the matched string and process each
        for(split ';', $1) {
            print $OUT "Intron\t{Translation\%", $_ ,"}\n";
        }
    }
}
## check status of close and print $! for descriptive error message
close($IN) or die "Can't close $infile. $!";
close($OUT) or die "Can't close $outfile. $!";
[download]

~Particle

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