To answer the question you asked by /msg, try the following:

while (my $line = <MYFILE>)
{
   chomp $line;

   # Do stuff here
}
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The problem is that $line was a global variable. strict complains about that, so you have to my the variable when you use it. The above is (almost) the standard way of handling a file line by line. The standard way most people do it would be to use $_ as much as possible. Something along the lines of:

while (<MYFILE>)
{
    # Skip commented-out lines (or whatever else you want to do)
    next if /^#/; 

    # Don't chomp unless we know we're going to use the line
    chomp;

    if (/SOME REGEX HERE/)
    {
        # Do stuff
    }
}
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Now, you don't want to chomp in the while condition. If you have a last line without a newline, that line will be skipped because chomp will indicate that it wasn't able to remove anything by returning undef.