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

use Data::Dumper;
use List::Util qw{ none };

my @rows;

while (<DATA>) {
    my @row = split ' ';
    push @rows, \@row;
}

print 'before: ', Dumper(\@rows);

@rows = grep { none { '9' eq $_ } @$_ } @rows;

print 'after: ', Dumper(\@rows);

__DATA__
2 2 0 1 0
2 2 0 2 1
0 2 1 1 0
0 1 1 1 0
2 2 0 0 0
2 9 0 2 1
0 2 0 1 0
2 2 0 9 0
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]

You don't even need a module. Just use grep to remove the rows/arrayrefs with missing data.

To check this assumption I have added an extra row of data "2 2 9 2 2". That row cannot match any of the other rows and therefore should not be deleted.

use Modern::Perl qw/2015/;

my %data;

# First we transform and load the data into a hash
while (<DATA>) {
    chomp;
    my $data = $_;
    s/([^9 ])/[$1X]/g;
    s/9/[0129]/g;
    s/X/9/g;
    $data{$_} = $data;
}

#Then we check if records with missing data are unique
for my $testrecord ( keys %data ) {
    next unless $data{$testrecord} =~ m/9/;
    for my $record ( keys %data ) {
        next if $data{$record} eq $data{$testrecord}; #don't check you
+rself
        if ( $data{$record} =~ m/$testrecord/ ) {
            delete $data{$testrecord};
            last;
        }
    }
}
say $data{$_} for keys %data;

__DATA__
2 2 0 1 0
2 2 0 2 1
0 2 1 1 0
0 1 1 1 0
2 2 0 0 0
2 9 0 2 1
0 2 0 1 0
2 2 0 9 0
2 2 9 2 2
[download]

0 1 1 1 0
0 2 0 1 0
2 2 0 1 0
2 2 0 0 0
2 2 0 2 1
0 2 1 1 0
2 2 9 2 2
[download]

Thanks for all the replies, unfortunately a simple grep won't work, as CountZero mentions - a row such as "2 2 9 2 2" would be considered unique, and should not be deleted.

the code provided by CountZero works perfectly, thanks once again for everybodys help!

Are you sure of your terminology? I may be wrong, but I understand imputation meaning filling in values for missing data, as opposed to excluding rows with missing data.

I like to filter data at the source.

use warnings;
use strict;
use Data::Dumper;

my @rows;
while (<DATA>) {
    my @row = grep { m/[012]/ } split ' ';
    push @rows, \@row if (scalar @row == 5);
}

print 'Results: ', Dumper(\@rows);

__DATA__
2 2 0 1 0
2 2 0 2 1
0 2 1 1 0
0 1 1 1 0
2 2 0 0 0
2 9 0 2 1
0 2 0 1 0
2 2 0 9 0
[download]

my $bad = 9;
my @filteredAoA = map { $bad ~~ @$_ ? () : [@$_] } @AoA;
[download]

Is a unique row determined by the combination or permutation of its members?

Update: The data the OP shows are unique if they are considered either as combinations or permutations, so I don't think the solutions shown would be correct if uniqueness were to be considered as combinations. Since we don't know the definition of uniqueness, I don't think we can define a solution yet.

See the update to my original post.