Read new format file: tab separated, and with display_label as 3rd column.

misc-scripts/analysis_description/load_analysis_descriptions.pl

@@ -16,21 +16,21 @@
 
  The script reads the analysis description file also found in this directory
  analysis.descriptions and loads the descriptions which match the logic names in
- the analysis table
+ the analysis table. Display labels are also set from this file.
 
  It will warn about analyses present in the database which don't have descriptions
- in the file
+ in the file.
 
 =head1 OPTIONS
 
-     Database options  
+     Database options
 
     -dbhost      host name for database (gets put as host= in locator)
     -dbport      For RDBs, what port to connect to (port= in locator)
     -dbname      For RDBs, what name to connect to (dbname= in locator)
     -dbuser      For RDBs, what username to connect as (dbuser= in locator)
     -dbpass      For RDBs, what password to use (dbpass= in locator)
-    -description_file path to file containing descriptions. The file 
+    -file        Path to file containing descriptions. The file 
                       analysis.descriptions in this directory can be used and is an 
                       example of the format
     -help print out documentation
@@ -58,15 +58,13 @@ my $dbname = '';
 my $file;
 my $help = 0;
 
-&GetOptions( 
-            'host|dbhost=s'      => \$dbhost,
-            'dbname=s'      => \$dbname,
-            'user|dbuser=s'      => \$dbuser,
-            'pass|dbpass=s'      => \$dbpass,
-            'port|dbport=s'      => \$dbport,
+&GetOptions('host|dbhost=s'       => \$dbhost,
+            'dbname=s'            => \$dbname,
+            'user|dbuser=s'       => \$dbuser,
+            'pass|dbpass=s'       => \$dbpass,
+            'port|dbport=s'       => \$dbport,
             'file|descriptions=s' => \$file,
-            'h|help!' => \$help,
-           );
+            'h|help!' => \$help);
 
 if(!$dbhost || !$dbname){
   print ("Need to pass in -dbhost $dbhost and -dbname $dbname\n");
@@ -85,55 +83,52 @@ if($help){
   useage();
 }
 
-
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor
-  (
-   -host   => $dbhost,
-   -user   => $dbuser,
-   -dbname => $dbname,
-   -pass   => $dbpass,
-   -port   => $dbport,
-  );
-
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host   => $dbhost,
+					    -user   => $dbuser,
+					    -dbname => $dbname,
+					    -pass   => $dbpass,
+					    -port   => $dbport);
 
 open(FH, $file) or throw("Failed to open $file $@");
-my $aa = $db->get_AnalysisAdaptor;
-my $analyses = $aa->fetch_all;
+my $aa = $db->get_AnalysisAdaptor();
+my $analyses = $aa->fetch_all();
 my %hash;
 foreach my $analysis(@$analyses){
-  $hash{lc($analysis->logic_name)} = $analysis;
+  $hash{lc($analysis->logic_name())} = $analysis;
 }
-LINE:while(<FH>){
-  /^(\S+)\s+(\S+)\s+(.+)/ and do {
-    my ($displayable, $logic_name, $description) = ($1, $2, $3);
-    #print "Parsed ".$displayable." ".$logic_name." ".$description."\n";
-    $description =~ s/^\s+//;
-    $description =~ s/\s+$//;
-
-    next if not $description;
-
-    if (exists $hash{lc($logic_name)}) {
-      my $analysis = $hash{lc($logic_name)};
-      
-      $analysis->description($description);
-      $analysis->displayable($displayable);
-      
-      my $display_label = $logic_name;
-      $display_label =~ s/_//g;
-      $analysis->display_label($display_label);
-
-      $aa->update($analysis);
-
-      delete $hash{lc($logic_name)};
-    }
+LINE:while(my $row = <FH>){
+
+  chomp($row);
+
+  next if ($row =~ /^#/);    # skip comments
+  next if ($row =~ /^$/);    # and blank lines
+  next if ($row =~ /^\s+$/); # and whitespace-only lines
+
+  my ($displayable, $logic_name, $display_label, $description) = split(/\t/, $row);
+  #print join("\t", $displayable, $logic_name, $display_label, $description, "\n");
+
+  $description =~ s/^\s+//;
+  $description =~ s/\s+$//;
+
+  next if not $description;
+
+  if (exists $hash{lc($logic_name)}) {
+    my $analysis = $hash{lc($logic_name)};
+
+    $analysis->description($description);
+    $analysis->displayable($displayable);
+    $analysis->display_label($display_label);
+
+    $aa->update($analysis);
+
+    delete $hash{lc($logic_name)};
   }
 }
 
 close(FH) or throw("Failed to close $file $@");
 
-if ( scalar(keys %hash)==0) { 
-  print "\nAll analysis descriptions have been updated, every analysis has a description now\n" ; 
+if ( scalar(keys %hash)==0) {
+  print "\nAll analysis descriptions have been updated, every analysis has a description now\n" ;
 }else{
   foreach my $k (keys %hash) {
     warning "No description was found for logic name $k ( ".$hash{$k}->dbID." ) \n";