Updated to schema 20 and now gene descriptions are not uppercased anymore....

Updated to schema 20 and now gene descriptions are not uppercased anymore. They are kept as in the original source. Also added -port option and updated the help menu

misc-scripts/gene_description/gene-descriptions.pl

@@ -37,10 +37,11 @@ my @word_order = qw(unknown hypothetical putative novel probable [0-9]{3} kDa fr
 ## Getting parameters/options and usage
 
 my $usage = "
- Usage: $0 -h host \\
-           -u dbuser \\
+ Usage: $0 -host host \\
+           -port port \\
+           -dbuser dbuser \\
            -debug \\
-           -d dbname 
+           -dbname dbname 
            -consortium dbname in external_db table (e.g. ZFIN_ID for zebrafish)
            -r regexps_file
            fileprotein_database_file(s) > gene-descriptions.tab
@@ -55,24 +56,26 @@ my $usage = "
 
  OR to load the data from gene-descriptions.tab file to \'gene-description\' table
 
-        $0 -h host \\
-           -u dbuser \\
-           -d dbname \\
-           -p password \\
+        $0 -host host \\
+           -port port \\
+           -dbuser dbuser \\
+           -dbname dbname \\
+           -dbpass password \\
            -load gene-descriptions.tab
 \n";
 
 my $help = 0;
-my ($host, $dbname, $dbuser, $dbpass, $gene_description_file);
+my ($host, $port, $dbname, $dbuser, $dbpass, $gene_description_file);
 my $regexp_file;
 my $debug = 0;
 my $consortium = "";
 
 unless (GetOptions('help' => \$help,
-		   'h=s' => \$host,
-		   'd=s' => \$dbname,
-		   'u=s' => \$dbuser,
-		   'p=s' => \$dbpass,
+		   'host=s' => \$host,
+		   'port=i' => \$port,
+		   'dbname=s' => \$dbname,
+		   'dbuser=s' => \$dbuser,
+		   'dbpass=s' => \$dbpass,
 		   'r=s' => \$regexp_file,
 		   'consortium' => \$consortium,
 		   'load=s' => \$gene_description_file,
@@ -121,7 +124,7 @@ if (defined $gene_description_file || defined $dbpass) {
 ## Loading data to database if requested and exit
 
 if (defined $gene_description_file) {
-  if (load_data($gene_description_file,$host,$dbname,$dbuser,$dbpass) == 1) {
+  if (load_data($gene_description_file,$host,$port,$dbname,$dbuser,$dbpass) == 1) {
     exit 0;
   } else {
     warn "Problem when loading data
@@ -147,6 +150,7 @@ exit 1";
 print STDERR "Connecting to $dbname $host......";
 
 my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor (-host => $host,
+                                             -port => $port,
 					     -dbname => $dbname,
 					     -user => $dbuser);
 print STDERR "Done\n";
@@ -161,11 +165,12 @@ print STDERR "Preparing query...";
 
 my $sth = $db->prepare("
 SELECT
- tsc.translation_id,tsc.gene_id,xdb.db_name,x.dbprimary_acc,ix.query_identity,ix.target_identity
+ tsl.translation_id,tsc.gene_id,xdb.db_name,x.dbprimary_acc,ix.query_identity,ix.target_identity
 FROM
- transcript tsc,object_xref ox,xref x,external_db xdb,identity_xref ix
+ translation tsl,transcript tsc,object_xref ox,xref x,external_db xdb,identity_xref ix
 WHERE
- tsc.translation_id = ox.ensembl_id AND
+ tsl.transcript_id = tsc.transcript_id AND
+ tsl.translation_id = ox.ensembl_id AND
  ox.xref_id = x.xref_id AND
  x.external_db_id = xdb.external_db_id AND
  xdb.db_name in ($db_query) AND
@@ -320,7 +325,7 @@ sub compare_desc {
 } # compare_desc
 
 sub load_data {
-  my ($gene_description_file,$host,$dbname,$dbuser,$dbpass) = @_;
+  my ($gene_description_file,$host,$port,$dbname,$dbuser,$dbpass) = @_;
 
   if (-e $gene_description_file) {
     symlink $gene_description_file,"$ENV{PWD}/gene_description_file.symlink";
@@ -331,6 +336,7 @@ exit 3";
   }
  
   my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor (-host => $host,
+                                               -port => $port,
 					       -dbname => $dbname,
 					       -user => $dbuser,
 					       -pass => $dbpass);
@@ -396,7 +402,7 @@ sub parse_protein_database {
       
       if ($line =~ /^DE\s{3}(\S.*\S)$/o) {
 	$desc .= " " unless ($desc eq "");
-	$desc .= uc $1;
+        $desc .= $1;
       }
       
       if ($line =~ /^\/\/$/o) {
@@ -410,11 +416,11 @@ sub parse_protein_database {
     } elsif ($db eq $protein_db_naming_href->{'refseq'}) {
       
       if ($line =~ /^DEFINITION\s+(\S.*\S)$/o) {
-	$desc .= uc $1;
+        $desc .= $1;
 	while (defined ($line = <PROTDBF>)) {
 	  last if ($line =~ /^ACCESSION\s+(\S+)\s*.*$/o);
 	  if ($line =~ /^\s+(\S.*\S)$/o) {
-	    $desc .= " ".uc $1;
+	    $desc .= " ". $1;
 	  }
 	}
       }