Merge branch '6.x-1.x' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-1.x

tripal_feature/api/tripal_feature.api.inc

@@ -824,13 +824,16 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   // if we are not getting the sequence from the parent sequence then
   // use what comes through from the feature record
   else {
-    $residues = $values->$field; 
+    $sql = "SELECT * FROM feature F WHERE feature_id = %d";
+    $values = db_fetch_object(chado_query($sql,$feature_id));
+    $residues = $values->residues;
     if ($output_format == 'fasta_html') {
        $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);  
     } 
     elseif ($output_format == 'fasta_txt') {
        $residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE);  
     }
+    $residues = ">$feature_name\n$residues\n";
   }
   
   // format the residues for display

tripal_feature/tripal_feature.drush.inc

@@ -79,7 +79,7 @@ function drush_tripal_feature_tripal_get_sequence() {
 
   // get the list of features
   $vars = array();
-  $sql  = "SELECT DISTINCT F.feature_id, F.name, F.uniquename ".
+  $sql  = "SELECT DISTINCT F.feature_id, F.name, F.uniquename, O.genus, O.species, CVT.name as feature_type ".
           "FROM feature F ".
           "  INNER JOIN organism O on O.organism_id = F.organism_id ".
           "  INNER JOIN cvterm CVT on CVT.cvterm_id = F.type_id ";
@@ -108,7 +108,7 @@ function drush_tripal_feature_tripal_get_sequence() {
   $q = chado_query($sql, $vars);
   while ($feature = db_fetch_object($q)) {
     $feature_id = $feature->feature_id;
-    $feature_name = $feature->name;
+    $feature_name = "$feature->uniquename $feature->name $feature->feature_type ($feature->genus $feature->species)";
       
     $sequence = tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
       $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,