Changeset 365

Timestamp:

05/29/10 23:38:33 (21 months ago)

Author:

AlexanderPico

Message:

Added HGNC symbol as primary id

Files:

• trunk/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl (modified) (2 diffs)

trunk/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl

@@ -840 +840 @@
                                              "\'http://www.genenames.org\'"],
                                 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 
-                                             'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 
+                                             'Alt VARCHAR(128) NOT NULL DEFAULT \'\'', 
                                              'Description VARCHAR(255) DEFAULT NULL',
                                              'Synonyms VARCHAR(255) DEFAULT NULL',
@@ -1899 +1899 @@
         elsif ($dbe_dbname =~ /^\'HGNC\'$/){  
             $ADMIN_Xrefs{$dbe_dbname}[10] = "\'Y\'"; # collected
-            if (!${$seen{HUGO}{$dbe_primary_id}}++){ 
-                $$GeneTables{HUGO}{$count.$dot.$subcount{HUGO}} = [$dbe_primary_id, $dbe_display_id, $dbe_description, $dbe_syns];
-                $$Ensembl_GeneTables{HUGO}{$count.$dot.$subcount{HUGO}} = [$gene_stable_id, $dbe_primary_id];
+            ## NOTE: working with symbols as primary id; storing numerical identifier as 'Alt' in attributes 
+            if (!${$seen{HUGO}{$dbe_display_id}}++){ 
+                $$GeneTables{HUGO}{$count.$dot.$subcount{HUGO}} = [$dbe_display_id, $dbe_primary_id, $dbe_description, $dbe_syns];
+                $$Ensembl_GeneTables{HUGO}{$count.$dot.$subcount{HUGO}} = [$gene_stable_id, $dbe_display_id];
                 #process Attributes
                 unless ($dbe_primary_id eq $dbe_display_id){
-                        $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}} = [$dbe_primary_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Symbol'), $dbe_display_id];
+                        $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}} = [$dbe_display_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Alt'), $dbe_primary_id];
                 }
                 #@syns = (@syns, $dbe_display_id);
-                $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Synonyms'), @syns];
-                $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}.$dot.'2'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Description'), $dbe_description];
+                $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}.$dot.'1'} = [$dbe_display_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Synonyms'), @syns];
+                $$Attributes{HUGO}{$count.$dot.$subcount{HUGO}.$dot.'2'} = [$dbe_display_id, mysql_quotes( $$GeneTables{HUGO}{'NAME'}[1]), mysql_quotes('Description'), $dbe_description];
                 ++$subcount{HUGO};
             }