#!/usr/bin/perl -w
use strict;
use File::Basename;
use Getopt::Std;
my $PROGRAM = basename $0;
my $USAGE=
"Usage: cat GENE_LIST | $PROGRAM
";

use DomRefine::Read;
use DomRefine::General;

### Settings ###
my %OPT;
getopts('D:', \%OPT);

if ($OPT{D}) {
    $ENV{'DOMREFINE_SEQ_DB'} = $OPT{D};
}

### Main ###
my @geneset = ();
-t and die $USAGE;
while (<STDIN>) {
    chomp;
    my @f = split;
    push @geneset, @f;
}
@geneset = sort {$a cmp $b} uniq(@geneset);
my @gene = get_genes_fused(\@geneset);

my %seq = ();
read_seq(\%seq, \@gene);
for my $geneset (@geneset) {
    my $seq = get_geneset_seq($geneset, \%seq);
    if ($seq) {
	print $seq;
    }
}
