Add synonym entries

svn path=/; revision=596

diff --git a/interactome_scripts/load_species_db.pl b/interactome_scripts/load_species_db.pl
index 45c5fa8255c83814ac52adedb4c87007548ee258..bdfce67ebaa1d8eca3eb7400978c53a5446b74fd 100755 (executable)
--- a/interactome_scripts/load_species_db.pl
+++ b/interactome_scripts/load_species_db.pl
@@ -47,14 +47,27 @@ foreach my $file (@files) {
        
        my ($retrieval_location, $retrieval_date) = retrieval_info($file);
        $retrieval_date =~ /(\d+)\_(\d+)\_(\d\d)/;
-       my $formatted_date = "20".$1."-".$2."-".$3;
+       my $formatted_date = "20".$3."-".$1."-".$2;
        
+       # insert version info into database.  If species previously entered, location and date will be updated.
        my $safe_info_table = $dbh->quote_identifier("version_info");
-       $dbh->do("insert into $safe_info_table (?,?,?)  on duplicate key update retrieval_location=$retrieval_location,date=$formatted_date",$species,$retrieval_location,$formatted_date);
+       # Create the database for version info if it doesn't already exist
+       $dbh->do("CREATE TABLE IF NOT EXISTS $safe_info_table (
+                       `species` varchar(255) NOT NULL,
+                       `retrieval_location` varchar(255) NOT NULL,
+                       `date` date NOT NULL,
+                       PRIMARY KEY (`species`)
+                       ) ENGINE=MyISAM");
+
+
+       $dbh->do("insert into $safe_info_table (species,retrieval_location,date) values ('$species','$retrieval_location','$formatted_date') on duplicate key update retrieval_location='$retrieval_location', date='$formatted_date'");
        
-       # create the database table
+       # create the database table for the species
        my $safe_table = $dbh->quote_identifier($species);
        
+       # create the database table for all synonyms
+       my $safe_syn_table = $dbh->quote_identifier('synonyms');
+       
        $dbh->do("drop table if exists $safe_table");
        $dbh->do("CREATE TABLE $safe_table (
                `gene_id` VARCHAR( 255 ) NOT NULL ,
@@ -62,16 +75,24 @@ foreach my $file (@files) {
                `sequence` TEXT NOT NULL ,
                UNIQUE ( `gene_id` )
                ) TYPE = MYISAM");
-               
+
+       $dbh->do("CREATE TABLE if NOT EXISTS  $safe_syn_table(
+                       `gene_id` VARCHAR( 255 ) NOT NULL ,
+                       `species` VARCHAR( 255 ) NOT NULL ,
+                       `synonyms` TEXT
+                       ) TYPE = MYISAM");
+
        # and the statement handler to do the inserts
        my $insert_sth = $dbh->prepare("insert into $safe_table (gene_id, gene_header, sequence) values (?,?,?)");
+       my $insert_syn_sth = $dbh->prepare("insert into $safe_syn_table (gene_id, species, synonyms) values (?,?,?)");
        
-       # create the variables:q!
+       # create the variables
        
        my %seq_hash; # keys is $gene, values are $seq and $gene_header
        my $gene;
        my $seq;
        my $gene_header;
+       my $synonyms;
        
        open(in_file,$file);
        
@@ -87,6 +108,7 @@ foreach my $file (@files) {
                        $gene_header =~ s/^>//;
                        $gene = find_gene($gene_header,$species);
                        $gene =~ s/^\>//;
+                       $synonyms = find_gene_synonym($gene_header,$species);
                        $seq = "";
                }else{
                        $seq = "$seq"."$line";
@@ -99,6 +121,10 @@ foreach my $file (@files) {
 
        foreach my $key (keys %seq_hash) {
                $insert_sth->execute($key,$seq_hash{$key}->{'gene_header'},$seq_hash{$key}->{'sequence'});
+
+               if($synonyms ne "null") {
+                               $insert_syn_sth->execute($key,$species,$synonyms);
+               }
        }
 }