changes related to stable_id merge

misc-scripts/alt_alleles/alt_alleles.pl

@@ -50,13 +50,12 @@ my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $vhost||'ens-staging
 #
 
 my $sql =(<<EOS);
-select aa.alt_allele_id, gsi.stable_id, x2.display_label
- from alt_allele aa, gene_stable_id gsi, xref x1, gene g
+select aa.alt_allele_id, g.stable_id, x2.display_label
+ from alt_allele aa, gene g, xref x1
      left join object_xref ox on g.gene_id = ox.ensembl_id
      left join xref x2 on ox.xref_id = x2.xref_id
      left join external_db edb on x2.external_db_id = edb.external_db_id
- where aa.gene_id = gsi.gene_id
-  and gsi.gene_id = g.gene_id
+ where aa.gene_id = g.gene_id
   and g.display_xref_id = x1.xref_id
   and ox.ensembl_object_type = 'Gene'
   and edb.db_name = 'ENSG';
@@ -130,7 +129,7 @@ my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $chost||'ens-staging
 
 my %stable_id_to_gene_id;
 
-$sth =  $core_dba->dbc->prepare("Select stable_id, gene_id from gene_stable_id");
+$sth =  $core_dba->dbc->prepare("Select stable_id, gene_id from gene");
 $sth->execute;
 my ($gene_id);
 $sth->bind_columns(\$core_stable_id, \$gene_id);
@@ -242,7 +241,7 @@ print "Added $alt_id_count alt_allele ids for $count genes\n";
 #
 # useful sql to look at sanity check problems
 #
-#select gsi.stable_id,g.seq_region_start, g.seq_region_end, s.name, x.display_label from gene g, seq_region s, gene_stable_id gsi, alt_allele aa, xref x where g.display_xref_id = x.xref_id and gsi.gene_id = g.gene_id and g.gene_id = aa.gene_id and g.seq_region_id = s.seq_region_id and aa.alt_allele_id =37;
+#select g.stable_id,g.seq_region_start, g.seq_region_end, s.name, x.display_label from gene g, seq_region s, alt_allele aa, xref x where g.display_xref_id = x.xref_id and g.gene_id = aa.gene_id and g.seq_region_id = s.seq_region_id and aa.alt_allele_id =37;
 
 
 
@@ -257,7 +256,7 @@ exit;
 
 
 ## LRG SQL. How to fit this in?
-##select ox.ensembl_id, gsi.gene_id from xref x, object_xref ox, external_db e, gene_stable_id gsi where x.xref_id = ox.xref_id and e.external_db_id = x.external_db_id and e.db_name like "Ens_Hs_gene" and ox.ensembl_object_type = "Gene" and x.display_label = gsi.stable_id ;
+##select ox.ensembl_id, g.gene_id from xref x, object_xref ox, external_db e, gene g where x.xref_id = ox.xref_id and e.external_db_id = x.external_db_id and e.db_name like "Ens_Hs_gene" and ox.ensembl_object_type = "Gene" and x.display_label = g.stable_id ;
 
 
 
@@ -266,13 +265,13 @@ exit;
 ##
 
 #$sql =(<<LRG);
-#SELECT  ox.ensembl_id, gsi.gene_id 
-#  FROM xref x, object_xref ox, external_db e, gene_stable_id gsi 
+#SELECT  ox.ensembl_id, g.gene_id 
+#  FROM xref x, object_xref ox, external_db e, gene g
 #    WHERE x.xref_id = ox.xref_id AND
 #          e.external_db_id = x.external_db_id AND
 #          e.db_name like "Ens_Hs_gene" AND
 #          ox.ensembl_object_type = "Gene" AND
-#           x.display_label = gsi.stable_id
+#           x.display_label = g.stable_id
 #LRG
 
 #$sth = $core_dba->dbc->prepare($sql);

misc-scripts/alternative_splicing/load_alt_splice_gff.pl

@@ -66,7 +66,7 @@ my %stable_id_to_dbid; # use for gene,transcripts and exons
 
 
 foreach my $type (qw(gene transcript exon)){
-  my $sth = $dbi->prepare("SELECT ".$type."_id, stable_id  FROM ".$type."_stable_id");
+  my $sth = $dbi->prepare("SELECT ".$type."_id, stable_id  FROM ".$type);
   $sth->execute;
   my ($stable_id, $dbid);
   $sth->bind_columns(\$dbid, \$stable_id);

misc-scripts/generate_stable_ids.pl

@@ -46,7 +46,6 @@ my $dbi =
   || die "Can't connect to database\n";
 
 foreach my $type (@types) {
-  my $table = $type . "_stable_id";
   my $sth;
 
   # Get starting stable ID, either specified or current max.
@@ -77,18 +76,17 @@ foreach my $type (@types) {
   # get a list of objects that don't currently have stable IDs assigned
   # and assign new ones, incrementing & preserving formatting as we go
   my $sql =
-      "SELECT $type.${type}_id "
+      "SELECT ${type}_id "
     . "FROM $type "
-    . "LEFT JOIN $table sid ON $type.${type}_id=sid.${type}_id "
-    . "WHERE sid.stable_id IS NULL";
+    . "WHERE stable_id IS NULL";
   $sth = $dbi->prepare($sql);
   $sth->execute();
 
   while ( my @row = $sth->fetchrow_array() ) {
     ( $new_stable_id, my $nis ) =
       @{ increment_stable_id( $new_stable_id, $type ) };
-    print(   "INSERT INTO $table "
-           . "VALUES($row[0],\'$nis\',1,\'$ts\',\'$ts\');\n" );
+    print(   "UPDATE $type SET stable_id = \'$nis\', version = 1, created_date = \'$ts\', modified_date = \'$ts\'"
+           . " WHERE ${type}_id = $row[0];\n" );
   }
 } ## end foreach my $type (@types)
 
@@ -154,19 +152,17 @@ sub get_max_stable_id_from_gene_archive {
 sub get_highest_stable_id {
   my ( $dbi, $type ) = @_;
 
-  my $sid = $type . "_stable_id";
-
   my ( $highest_from_current, $highest_from_archive );
 
   # Get highest stable ID from the relevant table.
 
-  my $sth = $dbi->prepare("SELECT MAX(stable_id) FROM $sid");
+  my $sth = $dbi->prepare("SELECT MAX(stable_id) FROM $type");
   $sth->execute();
 
   if ( my @row = $sth->fetchrow_array() ) {
     $highest_from_current = $row[0];
   } else {
-    die("Can't get max $type stable ID from $sid\n");
+    die("Can't get max $type stable ID from $type\n");
   }
 
   if ( length($highest_from_current) == 0 ) {
@@ -181,8 +177,7 @@ sub get_highest_stable_id {
     if ( length($highest_from_current) == 0 ) {
       print( "\n"
         . "WARNING:\n"
-        . "No exon_stable_id for exon found "
-        . "(exon_stable_id_table empty)\n"
+        . "No stable_id for exon found \n"
         . "I got no prefix to generate new stable_ids for type $type!!! "
         . "- I'll try to use gene_archive now\n" );
 
@@ -196,8 +191,8 @@ sub get_highest_stable_id {
         $prefix =~ s/G$//g;
       } else {
         die(  "ERROR: "
-            . "No entries in table exon_stable_id and "
-            . "table gene_archive found\n"
+            . "No entries in table exon and "
+            . "gene_archive tables found\n"
             . "Don't know which species prefix to use for species.\n" );
 
         $highest_from_current = sprintf( "%s%011d", $prefix, 0 );