Changeset 538

Timestamp:

07/04/11 02:03:20 (11 months ago)

Author:

AlexanderPico

Message:

additional tweaks to GO handling

Files:

• trunk/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl (modified) (4 diffs)

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

@@ -433 +433 @@
 my $dbname = $dbas[0]->dbc->dbname();        # e.g., core_mus_musculus_42_36c
 my @split_dbname = split(/_/, $dbname);
-if ($split_dbname[2] == "collection"){       # shift array elements for "collections"
+if ($split_dbname[2] eq "collection"){       # shift array elements for "collections"
         splice(@split_dbname,1,1);
 }
@@ -1763 +1763 @@
             $ADMIN_Xrefs{$dbe_dbname}[10] = "\'Y\'"; # collected
             if (!${$seen{GeneOntology}{$dbe_primary_id}}++){
-                # Get GO term annotations using $go_adaptor
                 my $name = mysql_quotes("");
                 my $namespace = mysql_quotes("");
+                # Get GO term annotations using $go_adaptor
                 if ($go_adaptor){
-                        my $acc = $dbe_primary_id;
-                        $acc =~ s/\'//g; # strip single quotes to use as variable
-                        my $term = $go_adaptor->fetch_by_accession($acc);
-                        my $name = mysql_quotes($term->name()); #e.g., plasma membrane
-                        my $namespace = mysql_quotes($term->namespace()); # e.g., cellular component
-                }       
-                $$GeneTables{GeneOntology}{$count.$dot.$subcount{GeneOntology}} = [$dbe_primary_id, $name, $namespace];
+                  my $acc = $dbe_primary_id;
+                  $acc =~ s/\'//g; # strip single quotes to use as variable
+                  my $term = $go_adaptor->fetch_by_accession($acc);
+                  my $name = mysql_quotes($term->name()); #e.g., plasma membrane
+                  my $namespace = mysql_quotes($term->namespace()); # e.g., cellular_component
+                  $dbe_description = $name unless ($name eq "" || !$name);
+                }
+                $$GeneTables{GeneOntology}{$count.$dot.$subcount{GeneOntology}} = [$dbe_primary_id, $dbe_description, $namespace];
                 $$Ensembl_GeneTables{GeneOntology}{$count.$dot.$subcount{GeneOntology}} = [$gene_stable_id, $dbe_primary_id];
-                $$Attributes{GeneOntology}{$count.$dot.$subcount{GeneOntology}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{GeneOntology}{'NAME'}[1]), mysql_quotes('Description'), $name]; 
+                $$Attributes{GeneOntology}{$count.$dot.$subcount{GeneOntology}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{GeneOntology}{'NAME'}[1]), mysql_quotes('Description'), $dbe_description]; 
                 ++$subcount{GeneOntology};
             }
@@ -1789 +1790 @@
                   my $namespace = mysql_quotes($term->namespace()); # e.g., cellular_component
                   if ($namespace =~ /\'biological_process\'/){
+                    if (!${$seen{GOslimBP}{$dbe_primary_id}}++){
                         $$GeneTables{GOslimBP}{$count.$dot.$subcount{GOslimBP}} = [$dbe_primary_id, $name];
                         $$Ensembl_GeneTables{GOslimBP}{$count.$dot.$subcount{GOslimBP}} = [$gene_stable_id, $dbe_primary_id];
                         $$Attributes{GOslimBP}{$count.$dot.$subcount{GOslimBP}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{GOslimBP}{'NAME'}[1]), mysql_quotes('Description'), $name];     
                         ++$subcount{GOslimBP};
+                    }
                   } elsif ($namespace =~ /\'cellular_component\'/){
+                    if (!${$seen{GOslimCC}{$dbe_primary_id}}++){
                         $$GeneTables{GOslimCC}{$count.$dot.$subcount{GOslimCC}} = [$dbe_primary_id, $name];
                         $$Ensembl_GeneTables{GOslimCC}{$count.$dot.$subcount{GOslimCC}} = [$gene_stable_id, $dbe_primary_id];
                         $$Attributes{GOslimCC}{$count.$dot.$subcount{GOslimCC}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{GOslimCC}{'NAME'}[1]), mysql_quotes('Description'), $name];
                         ++$subcount{GOslimCC};
+                    }
                   } elsif ($namespace =~ /\'molecular_function\'/){
+                    if (!${$seen{GOslimMF}{$dbe_primary_id}}++){
                         $$GeneTables{GOslimMF}{$count.$dot.$subcount{GOslimMF}} = [$dbe_primary_id, $name];
                         $$Ensembl_GeneTables{GOslimMF}{$count.$dot.$subcount{GOslimMF}} = [$gene_stable_id, $dbe_primary_id];
                         $$Attributes{GOslimMF}{$count.$dot.$subcount{GOslimMF}.$dot.'1'} = [$dbe_primary_id, mysql_quotes( $$GeneTables{GOslimMF}{'NAME'}[1]), mysql_quotes('Description'), $name];
                         ++$subcount{GOslimMF};
+                    }
                   } else {
                         #garbage?
@@ -2180 +2187 @@
   my %arrayTable = getArrayTable();
 
+if (!defined $arrayTable{$genus_species} ){
+        return;
+}
+
   foreach my $key ( keys %$GeneTables) {
       $subcount{$key} = 1;