#use local so that the setting doesn't interfere with
#other places you might want to read in data.
local $/='>';

#load sequences
my %hSequences;
while (my $line = <DATA>) {
  chomp $line;
  next if $line eq '';

  #extract data from record
  #  -- s at end of regex needed so that . matches new lines
  my ($subs, $gid, $sSequences)
    = $line
      =~ /^(\d+)_\d+\s+geneid(\d+)\s+\d+\s+\d+\slen=\d+\s+(.*)$/s;

  #populate hash
  my $sKey="$subs $gid";
  my $aSequences = $hSequences{$sKey};
  $hSequences{$sKey} = $aSequences = []
    unless defined($aSequences);
  push @$aSequences, split(/\s+/, $sSequences);
}

#print results
while (my ($k, $v) = each(%hSequences)) {
  $k =~ s/ / gid=/;
  print ">$k\n" . join("\n", sort @$v) . "\n";
}