I am currently trying to write a script which alters the contents of a 2D array. I first created a 2D array filled with '*':

********************
********************
********************
********************
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Then attempted to change parts of the 2D array based on y-value, x value and replacement string. So for instance, a change of (1, 2, "test) in the above array would yield

********************
**test**************
********************
********************
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This all worked fine, except that the arrays I was dealing with in the real world were 1.3-4 million columns x 100 rows. As you can imagine I pretty soon ran out of memory. So my next idea was to create an output file containing the '*' array and then use Tie::File and string manipulation to alter the rows, to save holding it all in memory. I then hit two problems with Tie::File (version 0.96). Using the following code from the CPAN documentation:

tie my @array, 'Tie::File', $outputFile or die $!;
my $line = $array[2];
print $line . "\n";
untie @array;
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Throws a "Use of uninitialized value in concatenation" error when printing the line, even though the outputFile contained 100 rows. The second problem I had was that using:

tie my @array, 'Tie::File', $outputFile or die $!;
$array[2] = 'This is a test';
untie @array;
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inserted 2 blank rows, then 'This is a test', then the original 100 rows. I was expecting it to simply replace the 3rd line. My complete code is here:

#!/usr/bin/perl
use strict;
use warnings;
use Tie::File;

my $genome_size = 1000; #1300000;
my $outputFile = "/Users/Benbo/Desktop/temp/template.txt";
unlink $outputFile if (-e $outputFile);
print "Start...\n";
add_fragment("Test", 2, 10, 200);
create_template();
print "Done\n";

sub add_fragment{
    my ($ref_id, $identity, $coord, $length) = @_;
    tie my @array, 'Tie::File', $outputFile or die $!;
    # $array[10] = 'This is a test';
    my $line = $array[2];
    print $line .  "\n";
    untie @array;
}

sub create_template{
    for (1..9){
        write_to_file($_ x 50 . "\n", $outputFile);
    }
}

sub write_to_file{
     my $input = shift;
     my $outputFile = shift;
     open my $output, ">>", "$outputFile" or die "Could not open $outp
+utFile: $!";
     print $output $input;
}
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So my first question is can anyone tell me what I'm doing wrong with Tie::File as it is not working as I thought it would from the CPAN docs. My second question is, given that I will be inserting around 300k fragments into the array, is there a quicker and more effcient way of doing this?