simple sanity check for human and mouse to make sure the core/vega links are...

simple sanity check for human and mouse to make sure the core/vega links are up to date with each other

misc-scripts/xref_mapping/core_vega_link_check.pl

+use Bio::EnsEMBL::Registry;
+use Bio::SeqIO;
+use strict;
+my $reg = "Bio::EnsEMBL::Registry";
+
+my $species = shift;
+
+if($species eq "mouse"){
+  
+  $reg->load_registry_from_db(
+			      -host => 'ens-staging2',
+			      -user => 'ensro');
+}
+else{
+  $reg->load_registry_from_db(
+			      -host => 'ens-staging1',
+			      -user => "ensro");
+}
+
+my $core_sa = $reg->get_adaptor($species,"core","slice");
+my $vega_sa = $reg->get_adaptor($species,"vega","slice");
+
+if(!defined($core_sa)){
+  die "Could not get core slice adaptor for $species???";
+}
+
+if(!defined($vega_sa)){
+  die "Could not get vega slice adaptor for $species???";
+}
+
+
+my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
+
+
+
+my $sth = $vega_sa->dbc->prepare($sql) || die "Could not prepare $sql for vega";
+
+
+my %vega_ott_to_enst;
+my %core_ott_to_enst;
+
+$sth->execute("ENST_CDS") or croak( $vega_sa->dbc->errstr() );
+while ( my @row = $sth->fetchrow_array() ) {
+  $vega_ott_to_enst{$row[0]} = $row[1];
+}
+
+$sth->execute("ENST_ident") or croak( $vega_sa->dbc->errstr() );
+while ( my @row = $sth->fetchrow_array() ) {
+  $vega_ott_to_enst{$row[0]} = $row[1];
+}
+
+print "We have from the vega database ".scalar(%vega_ott_to_enst)." ott to enst entries\n ";
+
+
+
+$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
+$sth->execute("OTTT") or croak( $core_sa->dbc->errstr() );
+my $core_extra_count = 0;
+while ( my @row = $sth->fetchrow_array() ) {
+  if(!defined($vega_ott_to_enst{$row[1]})){
+    $core_extra_count++;
+    if($core_extra_count < 10){
+      print "core extra ".$row[1]." ". $row[0]."\n";
+    }
+  }
+  $core_ott_to_enst{$row[1]} = $row[0];
+}
+print "Core extra tags (OTTT) -> $core_extra_count \n";
+$core_extra_count = 0;
+
+$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
+$sth->execute("shares_CDS_and_UTR_with_OTTT") or croak( $core_sa->dbc->errstr() );
+my $core_extra_count = 0;
+while ( my @row = $sth->fetchrow_array() ) {
+  if(!defined($vega_ott_to_enst{$row[1]})){
+    $core_extra_count++;
+    if($core_extra_count < 10){
+      print "core extra ".$row[1]." ". $row[0]."\n";
+    }
+  }
+  $core_ott_to_enst{$row[1]} = $row[0];
+}
+print "Core extra tags (shares_CDS_and_UTR_with_OTTT) -> $core_extra_count \n";
+$core_extra_count = 0;
+
+#$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
+#$sth->execute("shares_CDS_with_ENST") or croak( $core_sa->dbc->errstr() );
+#my $core_extra_count = 0;
+#while ( my @row = $sth->fetchrow_array() ) {
+#  if(!defined($vega_ott_to_enst{$row[1]})){
+#    $core_extra_count++;
+#    if($core_extra_count < 10){
+#      print "core extra ".$row[1]." ". $row[0]."\n";
+#    }
+#  }
+#  $core_ott_to_enst{$row[1]} = $row[0];
+#}
+#print "Core extra tags (shares_CDS_with_ENST) -> $core_extra_count \n";
+#$core_extra_count = 0;
+
+
+
+#$sth->execute("Vega_transcript") or croak( $core_sa->dbc->errstr() );
+#while ( my @row = $sth->fetchrow_array() ) {
+#  if(!($row[1] =~ /^OTT/)){
+#    next;
+#  }
+#  if(!defined($vega_ott_to_enst{$row[1]})){
+#    $core_extra_count++;
+#    if($core_extra_count < 10){
+#      print "core extra ".$row[1]." ". $row[0]."\n";
+#    }
+#  }
+#  $core_ott_to_enst{$row[1]} = $row[0];
+#}
+#print "Core extra tags (Vega_transcript) -> $core_extra_count \n";
+$core_extra_count = 0;
+
+$sth->execute("shares_CDS_with_OTTT") or croak( $core_sa->dbc->errstr() );
+while ( my @row = $sth->fetchrow_array() ) {
+  if(!($row[1] =~ /^OTT/)){
+    next;
+  }
+  if(!defined($vega_ott_to_enst{$row[1]})){
+    $core_extra_count++;
+    if($core_extra_count < 10){
+      print "core extra ".$row[1]." ". $row[0]."\n";
+    }
+  }
+  $core_ott_to_enst{$row[1]} = $row[0];
+}
+
+print "Core extra tags (shares_CDS_with_OTTT) -> $core_extra_count \n";
+$core_extra_count = 0;
+print "We have from the core database ".scalar(%core_ott_to_enst)." ott to enst entries\n ";
+
+
+
+my $vega_extra_count = 0;
+foreach my $key (keys %vega_ott_to_enst){
+  if(!defined($core_ott_to_enst{$key})){
+    $vega_extra_count++;
+    if($vega_extra_count < 10){
+      print "vega extra ".$key." ". $vega_ott_to_enst{$key}."\n";
+    }
+  }
+}
+
+print "Vega extra tags -> $vega_extra_count \n";
+