use Data::Dumper;

my $query;
while (<IN>) {
  if (s/^Query=\s*//) {
    my $save = $_;
    process($query); }
    $query = { query_line => $save };
  } elsif (m/(\d+)\s*letters/) {
    $query->{letters} = $1;
  } elsif (m/^gi/) {
    push(@{$query->{gi_lines}}, $_);
  }
}
process($query);

sub process {
  print Dumper($_[0]); # for now
}

##</code><code>##

sub process {
  my $query = shift;
  return unless $query; # first time $query will be undef
  ...
  # iterate through all the gi lines
  for my $gi_line (@{$query->{gi_lines}}) {
    if ($gi_line =~ m{\|ref\|}) { ... ref found ... }
  }
}