useful script to get the external databases references for a gene or...

useful script to get the external databases references for a gene or transcript using either the stable_id or the gene name

misc-scripts/xref_mapping/list_xrefs.pl

+use Bio::EnsEMBL::Registry;
+use Getopt::Long;
+use strict;
+my $reg = "Bio::EnsEMBL::Registry";
+
+
+
+my ($user, $pass, $host, $port, $dbname, $type, $stable_id);
+my ($species, $db_version, $ignore);
+
+GetOptions('user=s'        => \$user,
+           'pass=s'        => \$pass,
+           'host=s'        => \$host,
+           'port=i'        => \$port,
+           'dbname=s'      => \$dbname,
+           'type=s'        => \$type,
+           'species=s'     => \$species,
+           'version=s'  => \$db_version,
+           'id=s'          => \$stable_id,
+           'ignore=s'      => \$ignore,
+           'help'          => sub {usage(); exit(0); } );
+
+
+
+if(defined $species and defined $dbname){
+  die "You can only specify a species OR a dbname\n";
+}
+
+my %ignore_sources;
+if(defined $ignore){
+  foreach my $item (split(',',$ignore)){
+    $ignore_sources{$item} = 1;
+    print "ignoring $item sources\n";
+  }
+}
+if(defined $species){
+   $reg->load_registry_from_db( -host => $host || 'ensembldb.ensembl.org',
+                                -user => $user || 'anonymous',
+                                -db_version => $db_version || undef)
+}
+else{
+  new Bio::EnsEMBL::DBSQL::DBAdaptor(
+             -species => "test",
+	     -group   => 'core',
+             -host    => $host||'ensembldb.ensembl.org',
+	     -port    => $port||3306,
+             -user    => $user||'anonymous',
+	     -pass    => $pass||undef,
+             -dbname  => $dbname);
+  my $species = "test";
+}
+
+my $gene_adap =  $reg->get_adaptor($species,"core","gene");
+if(!defined($gene_adap)){
+  die "unable to connect to database and get adaptor\n";
+}
+my @transcripts ;
+if(lc($type) eq "gene"){
+  my $gene = $gene_adap->fetch_by_stable_id($stable_id);
+  if(!defined($gene)){
+    die "unable to find stable_id $stable_id\n";
+  }	
+  my $status = $gene->status;
+  my $display = $gene->display_xref;
+  if(defined($display)){
+    $display = $display->display_id;
+  }
+  else{
+    $display = "NO_DISPLAY_XREF";
+  }	
+  print "$status Gene $stable_id display = $display status = $status\n";
+  print "position\t".$gene->slice->seq_region_name."\n";
+  if(defined($gene->description)){
+    print $gene->description."\n";
+  }
+  my @db_entries = @{$gene->get_all_DBEntries()}; 
+  foreach my $entry (@db_entries){
+    if(!defined $ignore_sources{$entry->dbname}){
+      print "\t".$entry->dbname."\t".$entry->primary_id."\t".$entry->display_id."\t".$entry->info_text."\n";
+    }
+  }
+  @transcripts = @{$gene->get_all_Transcripts()};
+}	
+elsif(lc($type) eq "name"){
+  my @genes = @{$gene_adap->fetch_all_by_external_name($stable_id)};
+
+  foreach my $gene (@genes){
+    my $status = $gene->status;
+    my $display = $gene->display_xref;
+    if(defined($display)){
+      $display = $display->display_id;
+    }
+    else{
+      $display = "NO_DISPLAY_XREF";
+    }	
+    print "$status Gene $stable_id display = $display status = $status\n";
+    print "position\t".$gene->slice->seq_region_name."\n";
+    my @db_entries = @{$gene->get_all_DBEntries()}; 
+    foreach my $entry (@db_entries){
+      if(!defined $ignore_sources{$entry->dbname}){
+	print "\t".$entry->dbname."\t".$entry->primary_id."\t".$entry->display_id."\t".$entry->info_text."\n";
+      }
+    }
+    if(defined($gene->description)){
+      print $gene->description."\n";
+    }
+    push  @transcripts, @{$gene->get_all_Transcripts()};  
+  }
+}
+else{  
+  my $tran_adap =  $reg->get_adaptor($species,"core","transcript");
+  my $tran = $tran_adap->fetch_by_stable_id($stable_id);
+  push @transcripts, $tran; 
+}
+
+foreach my $tran (@transcripts){
+  my $display = $tran->display_xref;
+  if(defined($display)){
+    $display = $display->display_id;
+  }
+  else{
+    $display = "NO_DISPLAY_XREF";
+  }
+  print $tran->stable_id."\t".$display."\tstatus=".($tran->status||"NOT SET")."\n";
+  my @db_entries = @{$tran->get_all_DBLinks()};
+  foreach my $dbe (@db_entries){
+    if(!defined $ignore_sources{$dbe->dbname}){
+      print "\t*".$dbe->dbname."*\t".$dbe->primary_id."\t".$dbe->display_id."\t".$dbe->info_text."\n";
+    }
+  }
+}
+
+
+sub usage {
+
+print << 'EOF';
+
+  This script will report the external database references for a particular
+  gene or transcript. The gene or transcript is specified by setting the type
+  (gene, transcript or name) and also the identifier being looked up. i.e.
+  -type gene id ENSG00000053918
+  -type transcript ENST00000155840
+  -type name BRCA2
+
+
+  -species    The species you want to look at. This MUST be set unless you
+               use dbname
+
+  -type       Options are gene, transcript or name.(must be set)
+
+  -id         Identifier to look up. must be of the type specified above.
+
+  -ignore     external database source to ignore (seperated by comas)
+
+  -dbname     The database to look for the xrefs. (if species not set)
+
+  -user       The user to use to read the core database in ro mode 
+              (default anonymous)
+
+  -pass       The password for the user.
+
+  -host       The mysql server (default ensembldb.ensembl.org)
+
+  -version    Can be used to change the version of the database to be examined.
+              (only used when species is set)
+
+
+  Examples.
+
+  1) Find the external databases references for the human gene ENSG00000053918.
+
+     perl list_xrefs.pl -species human -type gene -id ENSG00000053918
+
+  2) Find the xrefs for the mouse gene that is named Cntnap1
+
+     perl list_xrefs.pl -species mouse -type name -id cntnap1
+
+  3) as above but we are not interested in GO or goslim_goa references
+
+     perl list_xrefs.pl -species mouse -type name -id cntnap1
+                        -ignore GO,goslim_goa
+
+EOF
+}
+
+