my desired output would be like this

# ID 1005.csv
C A C C A G G G G A C A A A A G G A etc..
C A C C A G G T G A C A C G G G A G etc..
etc...
[download]

the hash extends on for about another 1300 keys or so and the file that is being changed has about 800 more IDs<\p>

#!/usr/bin/perl
use warnings;
use strict;

my %hash = ( '5302' => [qw/C T/],
             '9046' => [qw/G A/],
            '11110' => [qw/T C/],
            '12640' => [qw/T C/],
            '18262' => [qw/A G/],
            '21994' => [qw/A G/],
            '25713' => [qw/A G/],
            '26638' => [qw/T G/],
            '28194' => [qw/A G/],
            '29841' => [qw/G A/],
            '30475' => [qw/T C/],
            '31503' => [qw/A C/],
            '32211' => [qw/G A/],
            '37138' => [qw/G A/],
            '41088' => [qw/G A/],
            '42626' => [qw/A G/]);

my @keys = sort { $a <=> $b } keys %hash;
while (<DATA>) {
    unless (index $_, '#') {
        print;
        next;
    }

    my $idx = 0;
    print join ' ', map {$hash{ $keys[$idx++] }[$_]} split;
    print "\n";
}


__DATA__
# ID 1005.csv
0 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0
0 1 1 1 0 1 1 0 1 1 1 0 0 0 0 0
# ID 1009.csv
0 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0
0 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0
[download]

I had to truncate the input since there are not enough entries in the sample hash.