tripal/tripal_analysis_unigene/tripal_analysis_unigene.module

<?php

function tripal_analysis_unigene_init(){
   // Add style sheet
   drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_unigene.css');
}
/**
*
*/
function tripal_analysis_unigene_node_info() {
	$nodes = array();
	$nodes['chado_analysis_unigene'] = array(
      'name' => t('Analysis: Unigene'),
      'module' => 'chado_analysis_unigene',
      'description' => t('A unigene assembly constructed from transcriptomic reads.'),
      'has_title' => FALSE,
      'title_label' => t('Analysis: Unigene'),
      'has_body' => FALSE,
      'body_label' => t('Unigene Analysis Description'),
      'locked' => TRUE
	);
	return $nodes;
}
/*******************************************************************************
 * Set the permission types that the chado module uses.  Essentially we
 * want permissionis that protect creation, editing and deleting of chado
 * data objects
 */
function tripal_analysis_unigene_perm(){
   return array(
      'access chado_analysis_unigene content',
      'create chado_analysis_unigene content',
      'delete chado_analysis_unigene content',
      'edit chado_analysis_unigene content',
   );
}

/*******************************************************************************
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 */
function chado_analysis_unigene_access($op, $node, $account){
   if ($op == 'create') {
      return user_access('create chado_analysis_unigene content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_analysis_unigene content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_analysis_unigene content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_analysis_unigene content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}
/**
*
*/
function chado_analysis_unigene_form ($node){

   // add in the default fields
   $form = chado_analysis_form($node);

   $unigene = $node->analysis->tripal_analysis_unigene;
   $unigene_name = $unigene->unigene_name;
   $num_reads    = $unigene->num_reads;
   $num_clusters = $unigene->num_clusters;
   $num_contigs = $unigene->num_contigs;
   $num_singlets = $unigene->num_singlets;

	$form['unigene_name'] = array(
      '#title' => t('Unigene Name'),
      '#type' => 'textfield',
      '#required' => TRUE,
      '#description' => t('A distinct name used to identify this unigene'),
      '#default_value' => $unigene_name,
	);

	$form['num_reads'] = array(
      '#title' => t('Number of Reads'),
      '#type' => 'textfield',
      '#required' => FALSE,
      '#description' => t('Provide the number of reads, after filtering that were used for input into the assembly'),
      '#default_value' => $num_reads,
	);

	$form['num_clusters'] = array(
      '#title' => t('Number of Clusters'),
      '#type' => 'textfield',
      '#required' => FALSE,
      '#description' => t('Provide the number of clusters generated by the asssembly if a clustering mechanism was used for unigene constructions'),
      '#default_value' => $num_clusters,
	);

	$form['num_contigs'] = array(
      '#title' => t('Number of Contigs'),
      '#type' => 'textfield',
      '#required' => FALSE,
      '#description' => t('Provide the number of contigs generated by the assembly'),
      '#default_value' => $num_contigs,
	);

	$form['num_singlets'] = array(
      '#title' => t('Number of Singlets'),
      '#type' => 'textfield',
      '#required' => FALSE,
      '#description' => t('Provide the number of singlets remaining in the assembly'),
      '#default_value' => $num_singlets,
	);
}
/**
*
*/
function chado_analysis_unigene_insert($node){
   // insert the analysis
   chado_analysis_insert($node);

   // add the unigene name as a property of the anslysis
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_type','tripal_analysis_unigene');	
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_name',$node->unigene_name);	
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);	
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_reads',$node->num_reads);	
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);	
   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_singlets',$node->num_clusters);	
}
/**
*
*/
function chado_analysis_unigene_update($node){
   chado_analysis_update($node); 

   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name,1);
   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs,1);
   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads,1);
   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters,1);
   tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets,1);   
}
/**
*
*/
function chado_analysis_unigene_delete($node){
  chado_analysis_delete($node);
}
/**
*
*/
function chado_analysis_unigene_view ($node, $teaser = FALSE, $page = FALSE) {
   // use drupal's default node view:
   $node = node_prepare($node, $teaser);
   return $node;
}
/**
*
*/
function chado_analysis_unigene_load($node){

   // load the default set of analysis fields
	$additions = chado_analysis_load($node);

   // create some variables for easier lookup
   $analysis = $additions->analysis;
   $analysis_id = $analysis->analysis_id;

   // add in the properties
   $unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
   $num_contigs  = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
   $num_reads    = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
   $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
   $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');

   $analysis->tripal_analysis_unigene->unigene_name = $unigene_name->value;
   $analysis->tripal_analysis_unigene->num_contigs = $num_contigs->value;
   $analysis->tripal_analysis_unigene->num_reads = $num_reads->value;
   $analysis->tripal_analysis_unigene->num_clusters = $num_clusters->value;
   $analysis->tripal_analysis_unigene->num_singlets = $num_singlets->value;

   // add in organism information using the materialized view
   $sql = "SELECT * FROM {organism_unigene_mview} OUM ".
          "  INNER JOIN {organism} O on OUM.organism_id = O.organism_id ".
          "WHERE OUM.analysis_id = %d ".
          "ORDER BY O.genus, O.species";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $organisms = db_query($sql,$analysis_id);
   tripal_db_set_active($previous_db);  // now use drupal database

   while($organism = db_fetch_object($organisms)){
      $sql = "SELECT nid FROM {chado_organism} WHERE organism_id = %d";
      $c_org = db_fetch_object(db_query($sql,$organism->organism_id));
      $organism->nid = $c_org->nid;
      $analysis->tripal_analysis_unigene->organisms[] = $organism;
   }


   return $additions;
}
/*******************************************************************************
 * tripal_analysis_unigene_nodeapi()
 * HOOK: Implementation of hook_nodeapi()
 * Display unigene results for allowed node types
 */
function tripal_analysis_unigene_nodeapi(&$node, $op, $teaser, $page) {

   switch ($op) {
      case 'view':
         // Find out which node types for showing the unigene
         $types_to_show = variable_get('tripal_analysis_unigene_setting',
            array('chado_feature','chado_organism'));

         // Abort if this node is not one of the types we should show.
         if (in_array($node->type, $types_to_show, TRUE)) {
            // Add unigene to the content item if it's not a teaser
            if ($teaser) {
               return '';
            }
         	
            // add the alignment to the feature search indexing
            if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
               $node->content['tripal_analysis_unigene_index_version'] = array(
						'#value' => theme('tripal_analysis_unigene_search_index',$node),
						'#weight' => 4,
               );
            } else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
               $node->content['tripal_analysis_unigene_index_version'] = array(
						'#value' => theme('tripal_analysis_unigene_search_result',$node),
						'#weight' => 4,
               );
            } else {

               if(strcmp($node->type,'chado_organism')==0){
                  $node->content['tripal_organism_unigenes'] = array(
					   	'#value' => theme('tripal_organism_unigenes', $node),
						   '#weight' => 4
                  );
               }
            }
         }
      break;   
   }
}
/************************************************************************
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 */
function tripal_analysis_unigene_theme () {
   return array(
      'tripal_analysis_unigene_search_index' => array (
         'arguments' => array('node'),
      ),
      'tripal_analysis_unigene_search_result' => array (
         'arguments' => array('node'),
      ),
      'tripal_organism_unigenes' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_organism_unigenes',
      ),
      'tripal_analysis_unigene_base' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_analysis_unigene_base',
      ),
   );
}

/*******************************************************************************
 *  
 */
function tripal_analysis_unigene_preprocess_tripal_organism_unigenes(&$variables){
   $node = $variables['node'];
   $organism = $node->organism;
   $unigenes = tripal_analysis_unigene_load_organism_unigenes($organism);
   $node->organism->tripal_analysis_unigene->unigenes =  $unigenes;
}
/************************************************************************
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object THAT WILL BE INDEXED.
 */
function theme_tripal_analysis_unigene_search_index ($node) {

   $feature = $node->feature;
   $obj_feature = tripal_analysis_unigene_get_alignments($feature);
   $alignments = $obj_feature->alignments;
   $content = "<strong>";
   if(count($alignments) > 0){
      // iterate through each alignment
      foreach ($alignments as $result){
         // EST alignments in chado use an EST_match type to map ESTs to
         // contigs and a rank to indicate the major srcfeature.
         // We don't want to show EST_matches on the alignment view
         // since that doesn't make much sense to the end user.  If this
         // is an EST_match and the feature is an EST then we want to show
         // the contig in the alignments.  The contig name is part of the
         // uniquename in the EST_match
         if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
            $sql = "SELECT srcfeature_id ".
                   "FROM {featureloc} ".
                   "WHERE feature_id = $result->feature_id ".
                   "ORDER BY rank";
            $previous_db = tripal_db_set_active ('chado');
            $contig_fid = db_result(db_query($sql));
            $sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
            $contig_name = db_result(db_query($sql));
            tripal_db_set_active($previous_db);
            $sql = "SELECT nid ".
                   "FROM {chado_feature} ".
                   "WHERE feature_id = $contig_fid";
            $contig_nid = db_result(db_query($sql));
            // Check if the EST exists as a drupal node. If yes, add a link to
            // it. If no, just show the name
            if ($contig_nid != 0) {
               $sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
               $node_exists = db_result(db_query($sql));
            }
            $content .= "$contig_name " ;
         }
         elseif($node->feature->cvname == 'contig' && $result->cvname == 'EST_match'){
            $sql = "SELECT vid ".
                   "FROM {node} ".
                   "WHERE title = '$result->feature_name'".
                   "ORDER BY vid DESC";
            // since the feature name is also the node title we can look it up
            $est_node = db_fetch_object(db_query($sql));
            $content .= "$result->feature_name ";
         }
         else {
            $content .= "$result->cvname $result->feature_name ";
         }
      }
   }
   $content .= "</strong>";
   return $content;
}

/************************************************************************
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object to show on a search result page.
 */
function theme_tripal_analysis_unigene_search_result ($node) {

   $feature = $node->feature;
   $obj_feature = tripal_analysis_unigene_get_alignments($feature);
   $alignments = $obj_feature->alignments;
   $content = "<strong>";
   if(count($alignments) > 0){
      // iterate through each alignment
      foreach ($alignments as $result){
         // EST alignments in chado use an EST_match type to map ESTs to
         // contigs and a rank to indicate the major srcfeature.
         // We don't want to show EST_matches on the alignment view
         // since that doesn't make much sense to the end user.  If this
         // is an EST_match and the feature is an EST then we want to show
         // the contig in the alignments.  The contig name is part of the
         // uniquename in the EST_match
         if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
            $sql = "SELECT srcfeature_id ".
                   "FROM {featureloc} ".
                   "WHERE feature_id = $result->feature_id ".
                   "ORDER BY rank";
            $previous_db = tripal_db_set_active ('chado');
            $contig_fid = db_result(db_query($sql));
            $sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
            $contig_name = db_result(db_query($sql));
            tripal_db_set_active($previous_db);
            $sql = "SELECT nid ".
                   "FROM {chado_feature} ".
                   "WHERE feature_id = $contig_fid";
            $contig_nid = db_result(db_query($sql));
            // Check if the EST exists as a drupal node. If yes, add a link to
            // it. If no, just show the name
            if ($contig_nid != 0) {
               $sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
               $node_exists = db_result(db_query($sql));
            }
            $content .= "Alignment to contig $contig_name. " ;
         }
         elseif($node->feature->cvname == 'contig' && $result->cvname == 'EST_match'){
            $sql = "SELECT vid ".
                   "FROM {node} ".
                   "WHERE title = '$result->feature_name'".
                   "ORDER BY vid DESC";
            // since the feature name is also the node title we can look it up
            $est_node = db_fetch_object(db_query($sql));
            $content .= "Aligned EST: $result->feature_name ";
         }
         else {
            $content .= "Aligned $result->cvname: $result->feature_name ";
         }
      }
   }
   $content .= "</strong>";
   return $content;
}

/*******************************************************************************
 * tripal_analysis_unigene_results ()
 * Prepare unigene result for the feature shown on the page
 */
function theme_tripal_analysis_unigene_feature_alignments($node) {
   $feature = $node->feature;
   $obj_feature = tripal_analysis_unigene_get_alignments($feature);
   $alignments = $obj_feature->alignments;
   if(count($alignments) > 0){
      $content = "<div id=\"tripal_analysis_unigene_box\" class=\"tripal_unigene-info-box\">";
      // we're showing contig alignments in GBrowse so create a link here for
      // that if this feature is a contig
      if($node->feature->cvname == 'contig'){
         $content .= "<div class=\"tripal_expandableBox\">".
                     "  <h3>ESTs in this contig</h3>".
                     "</div>";
         $content .= "<div class=\"tripal_expandableBoxContent\">";
      } else {
         $content .= "<div class=\"tripal_expandableBox\">".
                     "  <h3>Alignments</h3>".
                     "</div>";
         $content .= "<div class=\"tripal_expandableBoxContent\">";
      }
      $content .= "".
         "<table class=\"tripal_table_horz\">".
         "  <tr>".
         "    <th>Type</th>".
         "    <th>Feature</th>".
         "    <th align=\"right\">Position</th>".
         "  </tr>";
      // iterate through each alignment
      foreach ($alignments as $result){
         // EST alignments in chado use an EST_match type to map ESTs to
         // contigs and a rank to indicate the major srcfeature.
         // We don't want to show EST_matches on the alignment view
         // since that doesn't make much sense to the end user.  If this
         // is an EST_match and the feature is an EST then we want to show
         // the contig in the alignments.  The contig name is part of the
         // uniquename in the EST_match
         if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
            $sql = "SELECT srcfeature_id ".
                   "FROM {featureloc} ".
                   "WHERE feature_id = $result->feature_id ".
                   "ORDER BY rank";
            $previous_db = tripal_db_set_active ('chado');
            $contig_fid = db_result(db_query($sql));
            $sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
            $contig_name = db_result(db_query($sql));
            tripal_db_set_active($previous_db);
            $sql = "SELECT nid ".
                   "FROM {chado_feature} ".
                   "WHERE feature_id = $contig_fid";
            $contig_nid = db_result(db_query($sql));
            // Check if the EST exists as a drupal node. If yes, add a link to
            // it. If no, just show the name
            if ($contig_nid != 0) {
               $sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
               $node_exists = db_result(db_query($sql));
            }
            $content .=
              "<tr>".
              "  <td>Contig</td>".
              "  <td>";
            if ($node_exists != 0) {
               $content .= "<a href=\"".url("node/$contig_nid")."\">".
              	     	   "$contig_name</a>";
            } else {
               $content .= $contig_name;
            }
            $content .=
              "  </td>".
              "  <td align=\"right\">".
            number_format($result->fmin).
                   "-".
            number_format($result->fmax).
              "  </td>".
              "</tr>";
         }

         elseif($node->feature->cvname == 'contig' &&
         $result->cvname == 'EST_match'){
            $sql = "SELECT vid ".
                   "FROM {node} ".
                   "WHERE title = '$result->feature_name'".
                   "ORDER BY vid DESC";
            // since the feature name is also the node title we can look it up
            $est_node = db_fetch_object(db_query($sql));
            $content .=
              "<tr>".
              "  <td>EST</td>".
              "  <td>";
            //Check if the EST exists as a drupal node before adding a hyperlink
            if ($est_node->vid != 0) {
               $content .=
               	 "<a href=\"".url("node/$est_node->vid")."\">".
               $result->feature_name.
              	 "</a>";
            } else {
               $content .= $result->feature_name;
            }
            $content .=
              "  </td>".
              "  <td align=\"right\">".
            number_format($result->fmin).
                   "-".
            number_format($result->fmax).
              "  </td>".
              "</tr>";
         }
         else {
            $content .= "".
              "<tr>".
              "  <td>$result->cvname</td>".
              "  <td>$result->feature_name</td>".
              "  <td align=\"right\">$result->fmin</td>".
              "  <td align=\"right\">$result->fmax</td>".
              "  <td align=\"right\">$result->strand</td>".
              "</tr>";
         }
      }
      $content .= "</table>";

      /* if this is a contig then get the alignment
       if($node->feature->cvname == 'contig'){
       // get the directory prefix
       $prefix = preg_replace("/^(\d*)\d{3}$/","$1",$node->feature_id);
       if(!$prefix){
       $prefix = '0';
       }
       $data_url = variable_get('chado_feature_data_url','sites/default/files/data');
       $fh = fopen("$data_url/misc/$prefix/$node->feature->feature_id/alignment.txt", 'r');
       if($fh){
       $content .= "<b>Alignment:</b><div class=\"tripal_feature_assembly_alignment\"><pre>";
       while(!feof($fh)){
       $content .= fgets($fh);
       }
       $content .="</pre></div>";
       }
       fclose($fh);
       }
       */
      $content .= "</div></div>";
   }
   return $content;
}
/*******************************************************************************
*
*/
function tripal_analysis_unigene_get_alignments($map) {

   // get the alignments for this feature
   $sql = "SELECT F.name as feature_name, FL.fmin, FL.fmax, FL.strand, ".
          "  FL.phase, CVT.name as cvname, F.feature_id, F.uniquename, ".
          "  FL.featureloc_id ".
          "FROM {featureloc} FL ".
          "  INNER JOIN Feature F ON F.feature_id = FL.feature_id ".
          "  INNER JOIN Cvterm CVT ON CVT.cvterm_id = F.type_id ".
          "WHERE srcfeature_id = %d AND ".
          "  NOT(CVT.name = 'match' or CVT.name = 'match_part') ".
          "ORDER BY FL.fmin, FL.fmax";
   $previous_db = tripal_db_set_active('chado');
   $results = db_query($sql,$map->feature_id);
   $alignments = array();
   $i=0;
   while($subfeature = db_fetch_object($results)){
      $alignments[$i++] = $subfeature;
   }
   $additions->alignments = $alignments;

   /* get the GO Terms
    $sql = "SELECT DISTINCT * FROM {go_results_mview} ".
    "WHERE feature_id = %d";
    $results = db_query($sql,$map->feature_id);
    $go_terms = array();
    $i=0;
    while($term = db_fetch_object($results)){
    $go_terms[$i++] = $term;
    }
    $additions->go_terms = $go_terms;

    // get the feature properties
    $sql = "SELECT FP.value,FP.rank,CVT.name,CVT.definition ".
    "FROM {featureprop} FP".
    "  INNER JOIN Cvterm CVT ".
    "    ON FP.type_id = CVT.cvterm_id ".
    "WHERE feature_id = %d";
    $results = db_query($sql,$map->feature_id);
    $properties = array();
    $i=0;
    while($property = db_fetch_object($results)){
    $properties[$i++] = $property;
    }
    $additions->properties = $properties;
    */
   tripal_db_set_active($previous_db);
   return $additions;
}
/************************************************************************
*
*/   
function tripal_analysis_unigene_load_organism_unigenes($organism){

   // get information about this assemblies and add it to the items in this node
   $sql = "SELECT * FROM {organism_unigene_mview} OUM ".
          "  INNER JOIN {analysis} A  ON A.analysis_id = OUM.analysis_id ".
          "WHERE OUM.organism_id = %d ".
          "ORDER BY A.timeexecuted DESC";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$organism->organism_id);
   tripal_db_set_active($previous_db);  // now use drupal database

   $unigenes = array();
   $i=0;
   $sql = "SELECT nid FROM {chado_analysis} WHERE analysis_id = %d";
   while($unigene = db_fetch_object($results)){
      $analysis_id = $unigene->analysis_id;
      $c_node = db_fetch_object(db_query($sql,$analysis_id));
      if($c_node){  
         $unigene->nid = $c_node->nid;
      }
      // add in the properties
      $unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
      $num_contigs  = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
      $num_reads    = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
      $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
      $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
      
      $unigene->unigene_name = $unigene_name->value;
      $unigene->num_reads = $num_reads->value;
      $unigene->num_clusters = $num_clusters->value;
      $unigene->num_contigs = $num_contigs->value;     
      $unigene->num_singlets = $num_singlets->value;

      $unigenes[$i++] = $unigene;
   }
   return $unigenes;
}
/*******************************************************************************
 * Tripal Unigene administrative setting form. This function is called by
 * tripal_analysis module which asks for an admin form to show on the page
 */
function tripal_analysis_unigene_get_settings() {
   // Get an array of node types with internal names as keys
   $options = node_get_types('names');
   // Add 'chado_feature' to allowed content types for showing unigene results
   $allowedoptions ['chado_feature'] = "Show 'ESTs in this contig' on feature pages";
   $allowedoptions ['chado_organism'] = "Show assemblies on organism pages";

   $form['description'] = array(
       '#type' => 'item',
       '#value' => t("This option allows user to display the unigene assembly ".
          "information. For contigs, this would include an alignment and for ".
          "organisms this would be a list of assemblies. Check the box to ".
          "enable the display of unigene information. Uncheck to disable."),
		 '#weight' => 0,
   );

   $form['tripal_analysis_unigene_setting'] = array(
      '#type' => 'checkboxes',
      '#options' => $allowedoptions,
      '#default_value'=>variable_get('tripal_analysis_unigene_setting',array()),
   );
   $settings->form = $form;
   $settings->title = "Tripal Unigene";
   return $settings;
}