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#!/usr/bin/env perl
#Copyright (c) 2010 Joachim Bargsten <code at bargsten dot org>. All rights reserved.

use warnings;
use strict;

use 5.010;
use Carp;
use Bio::SeqIO;
use File::stat;
use Getopt::Long;

my $only_header;

GetOptions( 'only-header|oh|o' => \$only_header ) or die "Fehler im System";

my ( $file1, $file2 ) = @ARGV;
die "$file1 is no file" unless ( -f $file1 );
die "$file2 is no file" unless ( -f $file2 );

my $first_file_in_mem;
my ( $load_in_memory, $from_disk );
if ( stat($file1)->size > stat($file2)->size ) {
    $load_in_memory = $file2;
    $from_disk      = $file1;
} else {
    $load_in_memory    = $file1;
    $first_file_in_mem = 1;
    $from_disk         = $file2;
}

my %memory_seq;
{
    my $sin = Bio::SeqIO->new(
        -format => 'fasta',
        -file   => $load_in_memory,
    );

    while ( my $so = $sin->next_seq ) {
        ( my $seq = $so->seq ) =~ s/[^\w]//g;
        $memory_seq{$seq} = $so;
    }
}

my $sin = Bio::SeqIO->new(
    -format => 'fasta',
    -file   => $from_disk,
);

my $sout = Bio::SeqIO->new(
    -format => 'fasta',
    -fh     => \*STDOUT,
);

say STDERR "--- $file1";
say STDERR "+++ $file2";

while ( my $so = $sin->next_seq ) {
    ( my $seq = $so->seq ) =~ s/[^\w]//g;

    if ( exists( $memory_seq{$seq} ) && $memory_seq{$seq} ) {
        my ( $new_id, $new_desc );
        if ($first_file_in_mem) {
            $new_id   = $memory_seq{$seq}->display_id . '<=>' . $so->display_id;
            $new_desc = $memory_seq{$seq}->desc . '<=>' . $so->desc;

        } else {
            $new_id   = $so->display_id . ' <=> ' . $memory_seq{$seq}->display_id;
            $new_desc = $so->desc . ' <=> ' . $memory_seq{$seq}->desc;

        }

        $so->display_id( '=' . $new_id );
        $so->desc($new_desc);
        undef $memory_seq{$seq};
        die unless ( exists( $memory_seq{$seq} ) );
    } elsif( exists($memory_seq{$seq}) ) {
        say STDERR "Found sequence " . $so->display_id ." two times, skipping it";
    } else {
        if ($first_file_in_mem) {
            $so->display_id( '+' . $so->display_id );

        } else {