I'd recommend Getopt::Long. It's easy to use, and easier to extend. 
use Getopt::Long   qw( GetOptions );
use File::Basename qw( basename );

sub usage {
   my ($msg) = @_;
   print STDERR $msg if defined($msg);
   my $fn = basename($0);
   print STDERR "usage: $fn ...\n";    # XXX Fill in the "..."
   exit(1);
}

GetOptions(
   'a=s' => my $alignment_file,
   's=s' => my $scorecons_file,
   'i=s' => my $image_file,
   'm=s' => my $numbered_model,
   'c=s' => my $csa_file,
) or usage();

defined($alignment_file) or usage("Missing alignment file\n");
defined($scorecons_file) or usage("Missing score file\n");
defined($image_file    ) or usage("Missing image file\n");
defined($numbered_model) or usage("Missing numbered model file\n");
defined($csa_file      ) or usage("Missing CSA file\n");

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In reply to Re: Use of uninitialized value in concatenation (.) or string error after adding new arguement on command line by ikegami
in thread Use of uninitialized value in concatenation (.) or string error after adding new arguement on command line by Angharad

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