## Input the matrix text file: 
print "\n\n Please type the filename(.txt) i.e. d1.txt: ";
 $DNAfilename = <STDIN>;
 chomp $DNAfilename;         
## To remove white space:
$DNAfilename=~ s/\s//gis;
# open the file, or exit
 unless ( open(DNAFILE, $DNAfilename) ) {
 print "Cannot open file \"$DNAfilename\"\n\n";
 exit;
 } # Line 10
 @a = <DNAFILE>;
@m2=@a;

##</code><code>##

my @m2;
## Input the matrix text file:
print "\n\n Please type the filename(.txt) i.e. d1.txt: ";
chomp( my $filename = <STDIN> );

open my $fh, '<', $filename or die "can't open file $!";
while (<$fh>) {
    push @m2, [ split /,/, $_ ];
}
close $fh or die "can't close file: $!";