my $dir = '/path/to/data/directory'; my %hash; opendir my $DH, $dir or die "cannot open '$dir' $!"; while (my $file = readdir $DH ) { next if $file =~ /~$/; next if -d $file; open my $FH, "<", "$dir/$file" or die "Cannot open '$dir/$file' $!"; while ( my $line = <$FH> ) { next if /^#/ || !length($line); my ($key, @values ) = split(/\t/, $line); $hash{ $file }{ $key } = \@values; } }