Does your script start like this and have 700+ lines ?

#!/gpsr/local/bin/perl
use Getopt::Std;
getopts('i:o:');
$infile=$opt_i;
$outfile=$opt_o;

if($infile eq "" or $outfile eq "")
{
        print "\t./algpred.pl -i input_file -o output_file\n\n";
        print "\t-i:\tinput file in fasta format\n";
        print "\t-o:\toutput file\n";
        print "\n\tExample: ./algpred.pl -i /gpsr/examples/example.fas
+ta -o out.algpred\n";
        exit;
}
$ptnnum = `grep -c "^>" $infile`; chomp($ptnnum);
if($ptnnum > 1)
{
        print "\tDon't Enter multiple sequences... Enter single sequen
+ce fasta file\n";
        exit;
}
[download]

Are you asking how to run this script many times using a different inputfile each time ?