Changeset 548

Timestamp:

11/22/11 02:22:51 (6 months ago)

Author:

AlexanderPico

Message:

switched from $EnSpeciesCode? to En

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

@@ -198 +198 @@
 my $speciesPick = $splitPick[0];                              # store common name, e.g., Mouse
 my $twoLetterSpecies = $speciesTable{$speciesPick}[3];        # two-letter code, e.g., Mm
-my $EnSpeciesCode = "En".$twoLetterSpecies;                   # Ensembl species-specific codes, e.g., EnMm
+#my $EnSpeciesCode = "En".$twoLetterSpecies;                  # Ensembl species-specific codes, e.g., EnMm
 my $species = $speciesTable{$speciesPick}[0];                 # store genus species, e.g., Mus musculus 
 my @split_species = split(/\s/, $species);                    # split: [0]=genus, [1]=species, [2]=extra
@@ -1061 +1061 @@
         #####################################################################################
         foreach my $key ( keys %GeneTables){
-            %{$Ensembl_GeneTables{$key}} = ('NAME' => ["Ensembl_${$GeneTables{$key}}{NAME}[0]", "$EnSpeciesCode", "${$GeneTables{$key}}{NAME}[1]"], 
+            %{$Ensembl_GeneTables{$key}} = ('NAME' => ["Ensembl_${$GeneTables{$key}}{NAME}[0]", 'En', "${$GeneTables{$key}}{NAME}[1]"], 
                                             'HEADER' => ["\`Primary\` VARCHAR(128) NOT NULL DEFAULT \'\'", 
                                                          "\`Related\` VARCHAR(128) NOT NULL DEFAULT \'\'", 
@@ -1083 +1083 @@
         # but there is no need to use these Hash names as variables as with Gene Tables.  #
         ###################################################################################
-        %Ensembl = ('NAME' => ['Ensembl', "$EnSpeciesCode"], 
+        %Ensembl = ('NAME' => ['Ensembl', 'En'], 
                     'SYSTEM' => ["\'Ensembl (EBI, Sanger)\'", "\'$dateArg\'", 
                                  "\'ID|Symbol\\\\sBF|Description\\\\BF|Chromosome\\\\BF\|\'", "\'\|$species\|\'", "\'$species\'", 
@@ -1166 +1166 @@
     $Ensembl{$count} = [$gene_stable_id, $gene_symbol, $gene_description, $gene_chr];
     #note: dummy subcount and subsubcount to support HoHoA sorting and parsing
-    $Attributes{Ensembl}{$count.$dot.'1'.$dot.'1'} = [$gene_stable_id, mysql_quotes($EnSpeciesCode), mysql_quotes('Symbol'), $gene_symbol];
-    $Attributes{Ensembl}{$count.$dot.'1'.$dot.'2'} = [$gene_stable_id, mysql_quotes($EnSpeciesCode), mysql_quotes('Description'), $gene_description];
-    $Attributes{Ensembl}{$count.$dot.'1'.$dot.'3'} = [$gene_stable_id, mysql_quotes($EnSpeciesCode), mysql_quotes('Chromosome'), $gene_chr];
+    $Attibutes{Ensembl}{$count.$dot.'1'.$dot.'1'} = [$gene_stable_id, mysql_quotes('En'), mysql_quotes('Symbol'), $gene_symbol];
+    $Attributes{Ensembl}{$count.$dot.'1'.$dot.'2'} = [$gene_stable_id, mysql_quotes('En'), mysql_quotes('Description'), $gene_description];
+    $Attributes{Ensembl}{$count.$dot.'1'.$dot.'3'} = [$gene_stable_id, mysql_quotes('En'), mysql_quotes('Chromosome'), $gene_chr];
 
     ## PRINT PROGRESS MESSAGE