tripal_feature_sequence.tpl.php

  1. 2.x tripal_feature/theme/templates/tripal_feature_sequence.tpl.php
  2. 3.x legacy/tripal_feature/theme/templates/tripal_feature_sequence.tpl.php
1 theme call to tripal_feature_sequence.tpl.php
tripal_feature_node_view in tripal_feature/includes/tripal_feature.chado_node.inc
Implements hook_node_view(). Acts on all content types.

File

tripal_feature/theme/templates/tripal_feature_sequence.tpl.php
View source
  1. <?php

  2. /*

  3.  * There are several ways that sequences can be displayed.  They can come from the 

  4.  * feature.residues column,  they can come from an alignment with another feature,

  5.  * they can come from a protein sequence that has relationship with this sequence,

  6.  * or they can come from sub children (e.g. CDS coding sequences).

  7.  *   

  8.  * This template will show all types depending on the data available.

  9.  *

  10.  */

  11. 

  12. $feature = $variables['node']->feature;

  13. 

  14. // number of bases per line in FASTA format

  15. $num_bases = 50; 

  16. 

  17. // we don't want to get the sequence for traditionally large types. They are

  18. // too big,  bog down the web browser, take longer to load and it's not

  19. // reasonable to print them on a page.

  20. $residues ='';

  21. if(strcmp($feature->type_id->name,'scaffold') !=0 and

  22.    strcmp($feature->type_id->name,'chromosome') !=0 and

  23.    strcmp($feature->type_id->name,'supercontig') !=0 and

  24.    strcmp($feature->type_id->name,'pseudomolecule') !=0) {

  25.   $feature = chado_expand_var($feature,'field','feature.residues');

  26.   $residues = $feature->residues;

  27. } 

  28. 

  29. // get the sequence derived from alignments

  30. $feature = $variables['node']->feature;

  31. $featureloc_sequences = $feature->featureloc_sequences;

  32. 

  33. if ($residues or count($featureloc_sequences) > 0) { 

  34. 

  35.   $sequences_html = '';  // a variable for holding all sequences HTML text

  36.   $list_items = array(); // a list to be used for theming of content on this page

  37.   

  38.   // ADD IN RESIDUES FOR THIS FEATURE

  39.   // add in the residues if they are present

  40.   if ($residues) {

  41.     $list_items[] = '<a href="#residues">' . $feature->type_id->name . ' sequence</a>';

  42.      

  43.     // format the sequence to break every 50 residues

  44.     $sequences_html .= '<a name="residues"></a>';

  45.     $sequences_html .= '<div id="residues" class="tripal_feature-sequence-item">';

  46.     $sequences_html .= '<p><b>' . $feature->type_id->name . ' sequence</b></p>';

  47.     $sequences_html .= '<pre class="tripal_feature-sequence">';

  48.     $sequences_html .= '>' . tripal_get_fasta_defline($feature, '', NULL, '', strlen($feature->residues)) . "<br>";

  49.     $sequences_html .= wordwrap($feature->residues, $num_bases, "<br>", TRUE);

  50.     $sequences_html .= '</pre>';

  51.     $sequences_html .= '<a href="#sequences-top">back to top</a>';

  52.     $sequences_html .= '</div>';

  53.     

  54.   }

  55.   

  56.   // ADD IN RELATIONSHIP SEQUENCES (e.g. proteins)

  57.   // see the explanation in the tripal_feature_relationships.tpl.php 

  58.   // template for how the 'all_relationships' is provided. It is this

  59.   // variable that we use to get the proteins.

  60.   $all_relationships = $feature->all_relationships;

  61.   $object_rels = $all_relationships['object'];

  62.   $has_coding_seq = 0;

  63.   $coding_seq = '';

  64.   foreach ($object_rels as $rel_type => $rels){

  65.     foreach ($rels as $subject_type => $subjects){

  66.       foreach ($subjects as $subject){

  67.         

  68.         // add in protein sequence if it has residues

  69.         if ($rel_type == 'derives from' and $subject_type == 'polypeptide') {

  70.           $protein = $subject->record->subject_id;

  71.           $protein = chado_expand_var($protein, 'field', 'feature.residues');

  72.           

  73.           if ($protein->residues) {

  74.             $list_items[] = '<a href="#residues">protein sequence</a>';

  75.             $sequences_html .= '<a name="protein-' . $protein->feature_id . '"></a>';

  76.             $sequences_html .= '<div id="protein-' . $protein->feature_id . '" class="tripal_feature-sequence-item">';

  77.             $sequences_html .= '<p><b>protein sequence of ' . $protein->name . '</b></p>';

  78.             $sequences_html .= '<pre class="tripal_feature-sequence">';

  79.             $sequences_html .= '>' . tripal_get_fasta_defline($protein, '', NULL, '', strlen($protein->residues)) . "\n";

  80.             $sequences_html .= wordwrap($protein->residues, $num_bases, "<br>", TRUE);

  81.             $sequences_html .= '</pre>';

  82.             $sequences_html .= '<a href="#sequences-top">back to top</a>';

  83.             $sequences_html .= '</div>';

  84.           }

  85.         }

  86.         

  87.         // If the CDS has sequences then concatenate those. The objects 

  88.         // should be returned in order of rank

  89.         if ($rel_type == 'part of' and $subject_type == 'CDS') {

  90.           $cds = $subject->record->subject_id;

  91.           $cds = chado_expand_var($cds, 'field', 'feature.residues');

  92.           if ($cds->residues) {

  93.             $has_coding_seq = 1;

  94.             $coding_seq .= $cds->residues;

  95.           }

  96.         }

  97.         

  98.         // add any other sequences that are related through a relationship

  99.         // and that have values in the 'residues' column

  100.         

  101.       }

  102.     }

  103.   }

  104.   

  105.   // CODING SEQUENCES FROM RELATIONSHIPS

  106.   // add in any CDS sequences.

  107.   if ($has_coding_seq) {

  108.     $list_items[] = '<a href="#coding_sequence">coding sequence </a>';

  109.     $sequences_html .= '<a name="coding_sequence"></a>';

  110.     $sequences_html .= '<div id="coding_sequence" class="tripal_feature-sequence-item">';

  111.     $sequences_html .= '<p><b>coding sequence</b></p>';

  112.     $sequences_html .= '<pre class="tripal_feature-sequence">';

  113.     $sequences_html .= wordwrap($coding_seq, $num_bases, "<br>", TRUE);

  114.     $sequences_html .= '</pre>';

  115.     $sequences_html .= '<a href="#sequences-top">back to top</a>';

  116.     $sequences_html .= '</div>';

  117.   }

  118.   

  119.   /* ADD IN ALIGNMENT SEQUENCES FOR THIS FEATURE

  120.    * For retreiving the sequence from an alignment we would typically make a call to

  121.    * chado_expand_var function.  For example, to retrieve all

  122.    * of the featurelocs in order to get the sequences needed for this template, the

  123.    * following function call would be made:

  124.    *

  125.    *   $feature = chado_expand_var($feature,'table','featureloc');

  126.    *

  127.    * Then all of the sequences would need to be retreived from the alignments and

  128.    * formatted for display below.  However, to simplify this template, this has already

  129.    * been done by the tripal_feature module and the sequences are made available in

  130.    * the variable: 

  131.    *

  132.    *   $feature->featureloc_sequences

  133.    */

  134.   if(count($featureloc_sequences) > 0){

  135.     foreach($featureloc_sequences as $src => $attrs){

  136.       // the $attrs array has the following keys

  137.       //   * id:  a unique identifier combining the feature id with the cvterm id

  138.       //   * type: the type of sequence (e.g. mRNA, etc)

  139.       //   * location:  the alignment location

  140.       //   * defline: the definition line

  141.       //   * formatted_seq: the formatted sequences

  142.       //   * featureloc:  the feature object aligned to

  143.       $list_items[] = '<a href="#' . $attrs['id'] . '">'. $feature->type_id->name . ' from alignment at  ' . $attrs['location'] . "</a>";

  144.       $sequences_html .= '<a name="' . $attrs['id'] . '"></a>';

  145.       $sequences_html .= '<div id="' . $attrs['id'] . '" class="tripal_feature-sequence-item">';

  146.       $sequences_html .= '<p><b>'. $feature->type_id->name . ' from alignment at  ' . $attrs['location'] .'</b></p>';

  147.       $sequences_html .= $attrs['formatted_seq'];

  148.       $sequences_html .= '<a href="#sequences-top">back to top</a>';

  149.       $sequences_html .= '</div>';

  150.     }

  151.     

  152.     // check to see if this alignment has any CDS. If so, generate a CDS sequence

  153.     $cds_sequence = tripal_get_feature_sequences(

  154.         array(

  155.           'feature_id' => $feature->feature_id,

  156.           'parent_id' => $attrs['featureloc']->srcfeature_id->feature_id,

  157.           'name' => $feature->name,

  158.           'featureloc_id' => $attrs['featureloc']->featureloc_id,

  159.         ),

  160.         array(

  161.           'width' => $num_bases,  // FASTA sequence should have $num_bases chars per line

  162.           'derive_from_parent' => 1, // CDS are in parent-child relationships so we want to use the sequence from the parent

  163.           'aggregate' => 1, // we want to combine all CDS for this feature into a single sequence

  164.           'sub_feature_types' => array('CDS'), // we're looking for CDS features

  165.           'is_html' => 1

  166.         )

  167.     );

  168.     if (count($cds_sequence) > 0) {

  169.       // the tripal_get_feature_sequences() function can return multiple sequences

  170.       // if a feature is aligned to multiple places. In the case of CDSs we expect

  171.       // that one mRNA is only aligned to a single location on the assembly so we

  172.       // can access the CDS sequence with index 0.

  173.       if ($cds_sequence[0]['residues']) {

  174.         $list_items[] = '<a href="#coding_' . $attrs['id'] . '">coding sequence from alignment at  ' . $attrs['location'] . "</a>";

  175.         $sequences_html .= '<a name="ccoding_' . $attrs['id'] . '"></a>';

  176.         $sequences_html .= '<div id="coding_' . $attrs['id'] . '" class="tripal_feature-sequence-item">';

  177.         $sequences_html .= '<p><b>Coding sequence (CDS) from alignment at  ' . $attrs['location'] . '</b></p>';

  178.         $sequences_html .= '<pre class="tripal_feature-sequence">';

  179.         $sequences_html .= '>' . tripal_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', $cds_sequence[0]['length']) . "<br>";

  180.         $sequences_html .= $cds_sequence[0]['residues'];

  181.         $sequences_html .= '</pre>';

  182.         $sequences_html .= '<a href="#sequences-top">back to top</a>';

  183.         $sequences_html .= '</div>';

  184.       }

  185.     }

  186.   } 

  187.   ?>

  188. 

  189.   <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following sequences are available for this feature:</div> 

  190.   <?php

  191.   

  192.   // first add a list at the top of the page that can be formatted as the

  193.   // user desires.  We use the theme_item_list function of Drupal to create 

  194.   // the list rather than hard-code the HTML here.  Instructions for how

  195.   // to create the list can be found here:

  196.   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_item_list/7

  197.   print '<a name="sequences-top"></a>';

  198.   print theme_item_list(array(

  199.     'items' => $list_items,

  200.     'title' => '',

  201.     'type' => 'ul',

  202.     'attributes' => array(),

  203.   ));

  204. 

  205.   $message = 'Administrators, sequences will appear on this page if:

  206.     <br><br><b>For any feature type:</b>

  207.     <ul>

  208.       <li>This feature has residues stored in the "residues" field of the feature table of Chado.</li>

  209.       <li>This feature is aligned to another feature (e.g. scaffold, or chromosome). In this case, the

  210.           sequence underlying the alignment will be shown.</li>

  211.     </ul>

  212.     <br><b>For gene models:</b>

  213.     <ul>

  214.       <li>This feature has a "polypeptide" (protein) feature associated via the "feature_relationship" table of Chado with a

  215.           relationship of type "derives from" and the protein feature has residues. Typically, a protein

  216.           is associated with an mRNA feature and protein sequences will appear on the mRNA page.</li>

  217.       <li>This feature has one or more CDS features associated via the "feature_relationship" table of Chado with a

  218.           relationship of type "part of". If the CDS features have residues then those will be concatenated

  219.           and presented as a sequence. Typically, CDSs are associated with an mRNA feature and CDS sequences 

  220.           will appear on the mRNA page.</li>

  221.       <li>This feature is aligned to another feature (e.g. scaffold, or chromosome) and this feature has

  222.           one or more CDS features associated.  The CDS sequenes underlying the alignment will be

  223.           shown.</li>

  224.     </ul>

  225.     </p>';

  226.   print tripal_set_message($message, TRIPAL_INFO, array('return_html' => 1));

  227.   

  228.   // now print the sequences

  229.   print $sequences_html;

  230. }