project_display_xrefs.pl

use strict;

# Sets display_xref_ids for novel genes in the "to" database based
# on their orthologs in the "from" database. Can also project GO xrefs.
# Orthology relationships are read from a Compara database.

use Data::Dumper;
use Getopt::Long;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::GeneAdaptor;
use Bio::EnsEMBL::Utils::Eprof qw(eprof_start eprof_end eprof_dump);

my $method_link_type = "ENSEMBL_ORTHOLOGUES";

my %seen;

my ($conf, $registryconf, $version, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats, $descriptions, $release, $no_database, $quiet, $max_genes, $one_to_many, $go_check, $all_sources, $delete_only,  $to_species, $from_gene);

GetOptions('conf=s'          => \$conf,
	   'registryconf=s'  => \$registryconf,
	   'version=i'       => \$version,
	   'compara=s'       => \$compara,
	   'from=s'          => \$from_species,
	   'to=s'            => \@to_multi,
	   'method=s'        => \$method_link_type,
	   'names'           => \$names,
	   'go_terms'        => \$go_terms,
	   'print'           => \$print,
	   'delete_names'    => \$delete_names,
	   'delete_go_terms' => \$delete_go_terms,
	   'nobackup'        => \$no_backup,
	   'full_stats'      => \$full_stats,
           'descriptions'    => \$descriptions,
	   'release=i'       => \$release,
	   'no_database'     => \$no_database,
	   'quiet'           => \$quiet,
	   'max_genes=i'     => \$max_genes,
	   'one_to_many'     => \$one_to_many,
	   'go_check'        => \$go_check,
	   'all_sources'     => \$all_sources,
	   'delete_only'     => \$delete_only,
	   'help'            => sub { usage(); exit(0); });

$| = 1; # auto flush stdout

$descriptions = 1;

if (!$conf && !$registryconf && !$delete_only) {

  print STDERR "Configuration file must be supplied via -conf or -registryconf argument\n";
  usage();
  exit(1);

} elsif (!$from_species && !$delete_only)  {

  print STDERR "From species must be supplied via -from argument\n";
 usage();
  exit(1);

} elsif (!@to_multi) {

  print STDERR "At least one target species must be supplied via the -to argument\n";
  usage();

  exit(1);

} elsif (!$release && !$no_database) {

  print STDERR "Release must be specified via -release argument unless -no_database is used\n";