Moved code for generating sequence out of the sequence field handler and into an API function in the fature_module. Also created a drush command for extracting sequences

tripal_feature/api/tripal_feature.api.inc

@@ -508,23 +508,335 @@ function tripal_feature_delete_property_by_id($featureprop_id) {
  *
  * @ingroup tripal_feature_api
  */
- function trpial_feature_reverse_complement($sequence) {
-
-    $seq = strtoupper($sequence);
-    $seq = strrev($seq);
-    $seq = str_replace("A", "t", $seq);
-    $seq = str_replace("T", "a", $seq);
-    $seq = str_replace("G", "c", $seq);
-    $seq = str_replace("C", "g", $seq);
-    $seq = str_replace("Y", "r", $seq);
-    $seq = str_replace("R", "y", $seq);
-    $seq = str_replace("W", "w", $seq);
-    $seq = str_replace("S", "s", $seq);
-    $seq = str_replace("K", "m", $seq);
-    $seq = str_replace("M", "k", $seq);
-    $seq = str_replace("D", "h", $seq);
-    $seq = str_replace("V", "b", $seq);
-    $seq = str_replace("H", "d", $seq);
-    $seq = str_replace("B", "v", $seq);
-    return strtoupper($seq);
- }
+function trpial_feature_reverse_complement($sequence) {
+
+  $seq = strtoupper($sequence);
+  $seq = strrev($seq);
+  $seq = str_replace("A", "t", $seq);
+  $seq = str_replace("T", "a", $seq);
+  $seq = str_replace("G", "c", $seq);
+  $seq = str_replace("C", "g", $seq);
+  $seq = str_replace("Y", "r", $seq);
+  $seq = str_replace("R", "y", $seq);
+  $seq = str_replace("W", "w", $seq);
+  $seq = str_replace("S", "s", $seq);
+  $seq = str_replace("K", "m", $seq);
+  $seq = str_replace("M", "k", $seq);
+  $seq = str_replace("D", "h", $seq);
+  $seq = str_replace("V", "b", $seq);
+  $seq = str_replace("H", "d", $seq);
+  $seq = str_replace("B", "v", $seq);
+  return strtoupper($seq);
+}
+/**
+ * Retrieves the sequence for a feature.  
+ *
+ * @param $feature_id
+ *   The feature_id of the feature for which the sequence will be retrieved
+ * @param $feature_name
+ *   The feature name. This will appear on the FASTA definition line
+ * @param $num_bases_per_line
+ *   Indicate the number of bases to use per line.  A new line will be added
+ *   after the specified number of bases on each line.
+ * @param $derive_from_parent
+ *   Set to '1' if the sequence should be obtained from the parent to which
+ *   this feature is aligned.
+ * @param $aggregate
+ *   Set to '1' if the sequence should only contain sub features, excluding 
+ *   intra sub feature sequence.  For example, set this option to obtain just
+ *   the coding sequence of an mRNA.
+ * @param $output_format
+ *   The type of format.  Valid formats include 'fasta_html', 'fasta_txt' and 
+ *   'raw'.  The format 'fasta_txt' outputs line
+ *   breaks as <br> tags and the entire return value is in a <span> tag
+ *   with a fixed-width font definition.  'fasta_txt' outputs line breaks with
+ *   windows format carriage returns (e.g. \r\n) with no other formatting. The
+ *   raw format is simply the sequence with now FASTA formatting and no
+ *   line breaks.
+ * @param $upstream
+ *   An integer specifing the number of upstream bases to include in the output
+ * @param $downstream
+ *   An integer specifying the number of downstream bases to include in the 
+ *   output.
+ *
+ * @return
+ *   The DNA/protein sequence formated as requested.
+ *
+ * @ingroup tripal_feature_api
+ */
+function trpial_feature_get_formatted_sequence($feature_id, $feature_name, 
+  $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
+  $upstream, $downstream) {
+  
+  // to speed things up we need to make sure we have a persistent connection
+  tripal_db_persistent_chado(); 
+  
+  if (!$upstream) {
+     $upstream = 0;
+  }
+  if (!$downstream) {
+     $downstream = 0;
+  }
+  
+  // if we need to get the sequence from the parent but there is no aggregation
+  // then do so now.
+  if ($derive_from_parent) {             
+    
+    // execute our prepared statement
+    if (!tripal_core_is_sql_prepared('sequence_by_parent')) {
+      // prepare the queries we're going to use later during the render phase
+      // This SQL statement uses conditionals in the select clause to handle
+      // cases cases where the alignment is in the reverse direction and when
+      // the upstream and downstream extensions go beyond the lenght of the 
+      // parent sequence.
+      $psql ='PREPARE sequence_by_parent (int, int, int) AS 
+              SELECT
+                OF.name srcname, FL.srcfeature_id, FL.strand, OCVT.name as srctypename, SCVT.name as typename,
+                FL.fmin, FL.fmax,
+                CASE 
+                  WHEN FL.strand >= 0 THEN 
+                    CASE 
+                       WHEN FL.fmin - $1 <= 0 THEN 0
+                       ELSE FL.fmin - $1
+                    END
+                  WHEN FL.strand < 0 THEN
+                    CASE 
+                       WHEN FL.fmin - $2 <= 0 THEN 0
+                       ELSE FL.fmin - $2
+                    END                   
+                END as adjfmin,                                
+                                
+                CASE 
+                  WHEN FL.strand >= 0 THEN
+                    CASE 
+                      WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen 
+                      ELSE FL.fmax + $2
+                    END
+                  WHEN FL.strand < 0 THEN
+                    CASE
+                      WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen
+                      ELSE FL.fmax + $1   
+                    END               
+                END as adjfmax,     
+                
+                CASE 
+                  WHEN FL.strand >= 0 THEN 
+                    CASE 
+                       WHEN FL.fmin - $1 <= 0 THEN FL.fmin
+                       ELSE $1
+                    END
+                  ELSE
+                    CASE 
+                       WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen - FL.fmax
+                       ELSE $1
+                    END                   
+                END as upstream,
+                
+                CASE 
+                  WHEN FL.strand >= 0 THEN 
+                    CASE 
+                       WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen - FL.fmax
+                       ELSE $2
+                    END
+                  ELSE
+                    CASE 
+                       WHEN FL.fmin - $2 <= 0 THEN FL.fmin
+                       ELSE $2
+                    END                   
+                END as downstream,            
+                              
+                CASE 
+                  WHEN FL.strand >= 0 THEN 
+                    CASE 
+                       WHEN FL.fmin - $1 <= 0 THEN substring(OF.residues from 1 for ((FL.fmax - FL.fmin) + $1 + $2)) 
+                       ELSE substring(OF.residues from (FL.fmin + 1 - $1) for ((FL.fmax - FL.fmin) + $1 + $2))
+                    END
+                  WHEN FL.strand < 0 THEN
+                    CASE 
+                      WHEN FL.fmin - $2 <= 0 THEN substring(OF.residues from 1 for ((FL.fmax - FL.fmin) + $1 + $2)) 
+                      ELSE substring(OF.residues from (FL.fmin + 1 - $2) for ((FL.fmax - FL.fmin) + $1 + $2))      
+                    END
+                END as residues
+              FROM featureloc FL 
+                INNER JOIN feature SF on FL.feature_id = SF.feature_id
+                INNER JOIN cvterm SCVT on SF.type_id = SCVT.cvterm_id
+                INNER JOIN feature OF on FL.srcfeature_id = OF.feature_id                
+                INNER JOIN cvterm OCVT on OF.type_id = OCVT.cvterm_id
+              WHERE SF.feature_id = $3';
+              
+      $status = chado_query($psql);
+      if (!$status) {
+        watchdog('tripal_views_handler_field_sequence', 
+          "init: not able to prepare SQL statement '%name'", 
+          array('%name' => 'sequence_by_parent'), 'WATCHDOG ERROR');
+      }
+      // this query is meant to get all of the sub features of any given
+      // feature (arg #1) and order them as they appear on the reference
+      // feature (arg #2).
+      $psql ='PREPARE sub_features (int, int) AS 
+              SELECT SF.feature_id, CVT.name as type_name, SF.type_id
+              FROM feature_relationship FR
+                INNER JOIN feature SF on SF.feature_id = FR.subject_id
+                INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
+                INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
+                INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
+              WHERE FR.object_id = $1 and PF.feature_id = $2
+              ORDER BY FL.fmin ASC';
+              
+      $status = chado_query($psql);
+      if (!$status) {
+        watchdog('tripal_views_handler_field_sequence', 
+          "init: not able to prepare SQL statement '%name'", 
+          array('%name' => 'ssub_features'), 'WATCHDOG ERROR');
+      }
+      $psql ='PREPARE count_sub_features (int, int) AS 
+              SELECT count(*) as num_children
+              FROM feature_relationship FR
+                INNER JOIN feature SF on SF.feature_id = FR.subject_id
+                INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
+                INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
+                INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
+              WHERE FR.object_id = $1 and PF.feature_id = $2';
+              
+      $status = chado_query($psql);
+      if (!$status) {
+        watchdog('tripal_views_handler_field_sequence', 
+          "init: not able to prepare SQL statement '%name'", 
+          array('%name' => 'count_sub_features'), 'WATCHDOG ERROR');
+      }
+    }
+    
+    // execute the query
+    $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
+    $parents = chado_query($sql, $upstream, $downstream, $feature_id);
+    
+    while ($parent = db_fetch_object($parents)) {  
+      $seq = '';  // initialize the sequence for each parent
+
+      // if we are to aggregate then we will ignore the feature returned
+      // by the query above and rebuild it using the sub features
+      if ($aggregate){
+        
+        // now get the sub features that are located on the parent.
+        $sql = "EXECUTE sub_features (%d, %d)";
+        $children = chado_query($sql, $feature_id, $parent->srcfeature_id);
+        $sql = "EXECUTE count_sub_features (%d, %d)";
+        $num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id));
+               
+        // iterate through the sub features and concat their sequences. They
+        // should already be in order.
+        $types = array();
+        $i = 0;
+        while($child = db_fetch_object($children)) {
+          // keep up with the types
+          if (!in_array($child->type_name,$types)) {
+            $types[] = $child->type_name;
+          }
+          
+          $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
+
+          // if the first sub feature we need to include the upstream bases
+          if ($i == 0 and $parent->strand >= 0) {
+            // -------------------------- ref
+            //    ....---->  ---->        
+            //     up    1       2         
+            $q = chado_query($sql, $upstream, 0, $child->feature_id);
+          }
+          elseif ($i == 0 and $parent->strand < 0) {
+            // -------------------------- ref
+            //    ....<----  <----
+            //    down  1       2
+            $q = chado_query($sql, 0, $downstream, $child->feature_id);
+          }          
+          // if the last sub feature we need to include the downstream bases
+          elseif ($i == $num_children->num_children - 1 and $parent->strand >= 0) {
+            // -------------------------- ref
+            //        ---->  ---->....
+            //          1       2 down
+            $q = chado_query($sql, 0, $downstream, $child->feature_id);
+          }
+          elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) {
+            // -------------------------- ref
+            //        <----  <----....
+            //          1       2  up
+            $q = chado_query($sql, $upstream, 0, $child->feature_id);
+          }
+          
+          // for internal sub features we don't want upstream or downstream bases
+          else {         
+            $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
+            $q = chado_query($sql, 0, 0, $child->feature_id);
+          }
+          
+          while($subseq = db_fetch_object($q)){
+            // concatenate the sequences of all the sub features            
+            if($subseq->srcfeature_id == $parent->srcfeature_id){
+              $seq .= $subseq->residues;   
+            }
+          }                 
+          $i++;
+        } 
+      } 
+      // if this isn't an aggregate then use the parent residues
+      else {
+         $seq = $parent->residues;
+      }
+                            
+      // get the reverse compliment if feature is on the reverse strand
+      $dir = 'forward';
+      if ($parent->strand < 0) {
+        $seq = trpial_feature_reverse_complement($seq);
+        $dir = 'reverse';
+      }
+      
+      // now format for display
+      if ($output_format == 'fasta_html') {
+         $seq = wordwrap($seq, $num_bases_per_line, "<br>", TRUE);
+      } 
+      elseif ($output_format == 'fasta_txt') {
+         $seq = wordwrap($seq, $num_bases_per_line, "\n", TRUE);
+      }
+      $residues .= ">$feature_name ($parent->typename) $parent->srcname:" . ($parent->adjfmin + 1) . ".." . $parent->adjfmax ." ($dir). ";
+      if (count($types) > 0) {
+        $residues .= "Excludes all bases but those of type(s): " . implode(', ',$types) . ". " ;
+      }
+      if ($parent->upstream > 0) {
+         $residues .= "Includes " . $parent->upstream . " bases upstream.  ";
+      }
+      if ($parent->downstream > 0) {
+         $residues .= "Includes " . $parent->downstream . " bases downstream.  ";
+      }
+      if (!$seq) {
+        $residues .= "No sequence available\n<br>";          
+      }
+      else {
+        if ($output_format == 'fasta_html') {
+          $residues .= "<br>";
+        }
+        $residues .= "\n" . $seq . "\n";          
+        if ($output_format == 'fasta_html') {
+          $residues .= "<br>";
+        }
+      }
+    }
+  }
+  // if we are not getting the sequence from the parent sequence then
+  // use what comes through from the feature record
+  else {
+    $residues = $values->$field; 
+    if ($output_format == 'fasta_html') {
+       $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);  
+    } 
+    elseif ($output_format == 'fasta_txt') {
+       $residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE);  
+    }
+  }
+  
+  // format the residues for display
+  if($residues and $num_bases_per_line){
+    if ($output_format == 'fasta_html') {
+       $residues = '<span style="font-family: monospace;">' . $residues . '</span>';
+    }
+  }
+  return $residues;
+}

tripal_feature/tripal_feature.drush.inc

@@ -0,0 +1,104 @@
+<?php
+
+/**
+ * @file
+ * Contains function relating to drush-integration of this module.
+ */
+
+/**
+ * Describes each drush command implemented by the module
+ *
+ * @return
+ *   The first line of description when executing the help for a given command
+ */
+function tripal_feature_drush_help($command) {
+  switch ($command) {
+    case 'drush:tripal-get_sequence':
+      return dt('Prints sequences that match specified categories.');
+  }
+}
+
+/**
+ * Registers a drush command and constructs the full help for that command
+ *
+ * @return
+ *   And array of command descriptions
+ */
+function tripal_feature_drush_command() {
+  $items = array();
+  $items['tripal-get-sequence'] = array(
+    'description' => dt('Prints sequences that match specified categories.'),
+    'options'   => array(
+      'org'    => dt('The organism\'s common name. If specified, features for this organism will be retrieved.'),
+      'type'   => dt('The type of feature to retrieve (e.g. mRNA). All features that match this type will be retrieved.'),
+      'name'   => dt('The name of the feature to retrieve.'),
+      'up'     => dt('An integer value specifying the number of upstream bases to include.'),
+      'down'   => dt('An integer value specifying the number of downstream bases to incldue.'),
+      'out'    => dt('The output format. Valid options are "fasta_html", "fasta_txt" and raw.'),
+      'parent' => dt('Set this argument to 1 to retrieve the sequence from the parent in an alignment rather than the residues column of the feature itself.'),
+      'agg'    => dt('Set this argument to 1 to aggregate sub features into a single sequence.  This is useful, for example, for obtaining CDS sequence from an mRNA'),
+    ),
+    'examples' => array(
+      'Standard example' => 'drush tripal-current-job',
+    ),
+    'aliases' => array('trp-get-seq'),
+  );
+  return $items;
+}
+
+/**
+ * Executes jobs in the Tripal Jobs Queue
+ *
+ * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
+ */
+function drush_tripal_feature_tripal_get_sequence(){
+
+  $org_commonname = drush_get_option('org');  
+  $type = drush_get_option('type');
+  $feature_name = drush_get_option('name');
+  $upstream = drush_get_option('up');
+  $downstream = drush_get_option('down');
+  $output_format = drush_get_option('out');
+  $derive_from_parent = drush_get_option('parent');
+  $aggregate = drush_get_option('agg');
+  
+  if(!$output_format){
+     $output_format = 'fasta_txt';
+  }
+  
+  if(!$type and !$feature_name and !$org_commonname){
+     print "Please provide a type, feature name or organism common name\n";
+     return;
+  }
+
+  // get the list of features
+  $vars = array();
+  $sql = "SELECT DISTINCT F.feature_id, F.name ".
+         "FROM feature F ".
+         "  INNER JOIN organism O on O.organism_id = F.organism_id ".
+         "  INNER JOIN cvterm CVT on CVT.cvterm_id = F.type_id ".
+         "WHERE (1=1) ";
+  if ($org_commonname) {
+     $sql .= "AND O.common_name = '%s' ";
+     $vars[] = $org_commonname;
+  }
+  if ($type) {
+    $sql .= "AND CVT.name = '%s' ";
+    $vars[] = $type; 
+  }
+  if ($feature_name) {
+     $sql .= "AND F.name = '%s'";
+     $vars[] = $feature_name;
+  }
+  $num_bases_per_line = 50;
+  $q = chado_query($sql,$vars);
+  while($feature = db_fetch_object($q)){
+    $feature_id = $feature->feature_id;
+    $feature_name = $feature->name;
+      
+    $sequence = trpial_feature_get_formatted_sequence($feature_id, $feature_name, 
+      $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
+      $upstream, $downstream);
+    print $sequence;
+  }
+}

tripal_views/tripal_views.info

@@ -7,3 +7,5 @@ version = 6.x-1.0
 dependencies[] = views
 dependencies[] = ahah_helper
 dependencies[] = views_data_export
+dependencies[] = tripal_core
+

tripal_views/views/handlers/tripal_views_handler_field_sequence.inc

@@ -10,133 +10,8 @@
 class tripal_views_handler_field_sequence extends chado_views_handler_field {
 
   function init(&$view, $options) {
-    parent::init($view, $options);
-    
-    // to speed things up we need to make sure we have a persistent connection
-    tripal_db_persistent_chado(); 
-    
-    if (!tripal_core_is_sql_prepared('sequence_by_parent')) {
-      // prepare the queries we're going to use later during the render phase
-      // This SQL statement uses conditionals in the select clause to handle
-      // cases cases where the alignment is in the reverse direction and when
-      // the upstream and downstream extensions go beyond the lenght of the 
-      // parent sequence.
-      $psql ='PREPARE sequence_by_parent (int, int, int) AS 
-              SELECT
-                OF.name srcname, FL.srcfeature_id, FL.strand, OCVT.name as srctypename, SCVT.name as typename,
-                FL.fmin, FL.fmax,
-                CASE 
-                  WHEN FL.strand >= 0 THEN 
-                    CASE 
-                       WHEN FL.fmin - $1 <= 0 THEN 0
-                       ELSE FL.fmin - $1
-                    END
-                  WHEN FL.strand < 0 THEN
-                    CASE 
-                       WHEN FL.fmin - $2 <= 0 THEN 0
-                       ELSE FL.fmin - $2
-                    END                   
-                END as adjfmin,                                
-                                
-                CASE 
-                  WHEN FL.strand >= 0 THEN
-                    CASE 
-                      WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen 
-                      ELSE FL.fmax + $2
-                    END
-                  WHEN FL.strand < 0 THEN
-                    CASE
-                      WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen
-                      ELSE FL.fmax + $1   
-                    END               
-                END as adjfmax,     
-                
-                CASE 
-                  WHEN FL.strand >= 0 THEN 
-                    CASE 
-                       WHEN FL.fmin - $1 <= 0 THEN FL.fmin
-                       ELSE $1
-                    END
-                  ELSE
-                    CASE 
-                       WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen - FL.fmax
-                       ELSE $1
-                    END                   
-                END as upstream,
-                
-                CASE 
-                  WHEN FL.strand >= 0 THEN 
-                    CASE 
-                       WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen - FL.fmax
-                       ELSE $2
-                    END
-                  ELSE
-                    CASE 
-                       WHEN FL.fmin - $2 <= 0 THEN FL.fmin
-                       ELSE $2
-                    END                   
-                END as downstream,            
-                              
-                CASE 
-                  WHEN FL.strand >= 0 THEN 
-                    CASE 
-                       WHEN FL.fmin - $1 <= 0 THEN substring(OF.residues from 1 for ((FL.fmax - FL.fmin) + $1 + $2)) 
-                       ELSE substring(OF.residues from (FL.fmin + 1 - $1) for ((FL.fmax - FL.fmin) + $1 + $2))
-                    END
-                  WHEN FL.strand < 0 THEN
-                    CASE 
-                      WHEN FL.fmin - $2 <= 0 THEN substring(OF.residues from 1 for ((FL.fmax - FL.fmin) + $1 + $2)) 
-                      ELSE substring(OF.residues from (FL.fmin + 1 - $2) for ((FL.fmax - FL.fmin) + $1 + $2))      
-                    END
-                END as residues
-              FROM featureloc FL 
-                INNER JOIN feature SF on FL.feature_id = SF.feature_id
-                INNER JOIN cvterm SCVT on SF.type_id = SCVT.cvterm_id
-                INNER JOIN feature OF on FL.srcfeature_id = OF.feature_id                
-                INNER JOIN cvterm OCVT on OF.type_id = OCVT.cvterm_id
-              WHERE SF.feature_id = $3';
-              
-      $status = chado_query($psql);
-      if (!$status) {
-        watchdog('tripal_views_handler_field_sequence', 
-          "init: not able to prepare SQL statement '%name'", 
-          array('%name' => 'sequence_by_parent'), 'WATCHDOG ERROR');
-      }
-      // this query is meant to get all of the sub features of any given
-      // feature (arg #1) and order them as they appear on the reference
-      // feature (arg #2).
-      $psql ='PREPARE sub_features (int, int) AS 
-              SELECT SF.feature_id, CVT.name as type_name, SF.type_id
-              FROM feature_relationship FR
-                INNER JOIN feature SF on SF.feature_id = FR.subject_id
-                INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
-                INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
-                INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
-              WHERE FR.object_id = $1 and PF.feature_id = $2
-              ORDER BY FL.fmin ASC';
-              
-      $status = chado_query($psql);
-      if (!$status) {
-        watchdog('tripal_views_handler_field_sequence', 
-          "init: not able to prepare SQL statement '%name'", 
-          array('%name' => 'ssub_features'), 'WATCHDOG ERROR');
-      }
-      $psql ='PREPARE count_sub_features (int, int) AS 
-              SELECT count(*) as num_children
-              FROM feature_relationship FR
-                INNER JOIN feature SF on SF.feature_id = FR.subject_id
-                INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
-                INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
-                INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
-              WHERE FR.object_id = $1 and PF.feature_id = $2';
-              
-      $status = chado_query($psql);
-      if (!$status) {
-        watchdog('tripal_views_handler_field_sequence', 
-          "init: not able to prepare SQL statement '%name'", 
-          array('%name' => 'count_sub_features'), 'WATCHDOG ERROR');
-      }
-    }
+    parent::init($view, $options);  
+        
   }
 
   /**
@@ -242,6 +117,13 @@ class tripal_views_handler_field_sequence extends chado_views_handler_field {
        $downstream = 0;
     }
     
+    $derive_from_parent = $this->options['display']['derive_from_parent'];
+    $aggregate = $this->options['display']['aggregate'];
+    
+    $residues = trpial_feature_get_formatted_sequence($feature_id, $feature_name, 
+      $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
+      $upstream, $downstream);
+ /*   
     // if we need to get the sequence from the parent but there is no aggregation
     // then do so now.
     if ($this->options['display']['derive_from_parent']) {             
@@ -379,7 +261,7 @@ class tripal_views_handler_field_sequence extends chado_views_handler_field {
       if ($output_format == 'fasta_html') {
          $residues = '<span style="font-family: monospace;">' . $residues . '</span>';
       }
-    }
+    } */
     return $residues;         
   } 
 }