It would be helpful to handle these rogue entries.

Well, then, to modify tommyw's code:

use strict;

my (%hash, @G1_out, @G2_out);
my @rogues;
$hash{$_}=\@G1_out for qw(H0 H1); # etc
$hash{$_}=\@G2_out for qw(PX P2);

while (<>) {
  chomp;
  push @{$hash{substr($_, 0, 2)} || \@rogues}, $_;
}
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