Thanks Linuxer, Here are my changes, now the program finishes and I have no error message but I only have the locus_acc_no = printed out several times and it has no value. Thanks, B 
#!/usr/bin/perl -w
use strict;
use warnings;

use lib "/d/user2/aszend01/BCII/240213";
use ModuleMatching;

my $locus_acc_no = "";
my $key = 1;

print '$key = ', $key, "\n";


# test for not allowing more than one file to work on   
unless (1 == scalar(@ARGV)){
    die "two many files";
}
# test if the infile cannot be opened
open(IN, $ARGV[0])
    or die "unable to open input file $ARGV[0]\n";


while (my $line = <IN>) {
    # give the number of records a new key number started with 1 incre
+mented with 1 in each new record devided with "//" signs
    if ($line =~ /^\/\//){
        $key++;
        print '$key = ', $key, "\n";
        $locus_acc_no = "";
    }
    # locus_acc_no
    if ($line =~ ModuleMatching::MatchLAC($locus_acc_no)) {
        print "locus_acc_no ", $locus_acc_no;
#        print $2, "\n";
#        $hLocus_Acc{$key} = $1;
#        print "%hLocus_Acc{$key} = $1\n";
#        $hLength{$key} = $2;
#        print "%hLength{$key} = $2\n";
    }
}

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In reply to Re^2: matching problem by Balaton
in thread matching problem by Balaton

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