feature; // we don't want to get the sequence for traditionally large types. They are // too big, bog down the web browser, take longer to load and it's not // reasonable to print them on a page. $residues =''; if(strcmp($feature->type_id->name,'scaffold') !=0 and strcmp($feature->type_id->name,'chromosome') !=0 and strcmp($feature->type_id->name,'supercontig') !=0 and strcmp($feature->type_id->name,'pseudomolecule') !=0) { $feature = chado_expand_var($feature,'field','feature.residues'); $residues = $feature->residues; } // get the sequence derived from alignments $feature = $variables['node']->feature; $featureloc_sequences = $feature->featureloc_sequences; if ($residues or count($featureloc_sequences) > 0) { $sequences_html = ''; // a variable for holding all sequences HTML text $list_items = array(); // a list to be used for theming of content on this page ?>
The following sequences are available for this feature:
Current ' . $feature->type_id->name . ' sequence'; // format the sequence to break every 50 residues $sequences_html .= ''; $sequences_html .= '
'; $sequences_html .= '

Current ' . $feature->type_id->name . ' sequence

'; $sequences_html .= '
';
    $sequences_html .= '>' . tripal_get_fasta_defline($feature) . "\n";
    $sequences_html .= preg_replace("/(.{50})/","\\1
",$feature->residues);
    $sequences_html .= '
'; $sequences_html .= 'back to top'; $sequences_html .= '
'; } // ADD IN RELATIONSHIP SEQUENCES (e.g. proteins) // see the explanation in the tripal_feature_relationships.tpl.php // template for how the 'all_relationships' is provided. It is this // variable that we use to get the proteins. $all_relationships = $feature->all_relationships; $object_rels = $all_relationships['object']; $has_coding_seq = 0; foreach ($object_rels as $rel_type => $rels){ foreach ($rels as $subject_type => $subjects){ foreach ($subjects as $subject){ // add in protein sequence if it has residues if ($rel_type == 'derives from' and $subject_type == 'polypeptide') { $protein = $subject->record->subject_id; $protein = chado_expand_var($protein, 'field', 'feature.residues'); if ($protein->residues) { $list_items[] = 'Protein sequence of ' . $protein->name . ''; $sequences_html .= ''; $sequences_html .= '
'; $sequences_html .= '

Protein sequence of ' . $protein->name . '

'; $sequences_html .= '
';
            $sequences_html .= '>' . tripal_get_fasta_defline($protein) . "\n";
            $sequences_html .= preg_replace("/(.{50})/","\\1
", $protein->residues);
            $sequences_html .= '
'; $sequences_html .= 'back to top'; $sequences_html .= '
'; } } // we want to know if there are any coding sequences associated with this feature // if so we will use some code a bit later on to get those sequences if ($rel_type == 'part of' and $subject_type == 'CDS') { $has_coding_seq = 1; } // add any other sequences that are related through a relationship // and that have values in the 'residues' column } } } /* ADD IN ALIGNMENT SEQUENCES FOR THIS FEATURE * For retreiving the sequence from an alignment we would typically make a call to * chado_expand_var function. For example, to retrieve all * of the featurelocs in order to get the sequences needed for this template, the * following function call would be made: * * $feature = chado_expand_var($feature,'table','featureloc'); * * Then all of the sequences would need to be retreived from the alignments and * formatted for display below. However, to simplify this template, this has already * been done by the tripal_feature module and the sequences are made available in * the variable: * * $feature->featureloc_sequences */ if(count($featureloc_sequences) > 0){ foreach($featureloc_sequences as $src => $attrs){ // the $attrs array has the following keys // * src: a unique identifier combining the feature id with the cvterm id // * type: the type of sequence (e.g. mRNA, etc) // * location: the alignment location // * defline: the definition line // * formatted_seq: the formatted sequences $list_items[] = 'Alignment at ' . $attrs['location'] . ""; $sequences_html .= ''; $sequences_html .= '
'; $sequences_html .= '

Alignment at ' . $attrs['location'] .'

'; $sequences_html .= $attrs['formatted_seq']; $sequences_html .= 'back to top'; $sequences_html .= '
'; } } // CODING SEQUENCES // add in any CDS sequences. if ($has_coding_seq) { // use the tripal_get_sequence() API function to retreive the CDS sequences $cds_sequence = tripal_get_sequence( array( 'feature_id' => $feature->feature_id, 'name' => $feature->name, ), array( 'width' => 50, // FASTA sequence should have 50 chars per line 'derive_from_parent' => 1, // CDS are in parent-child relationships so we want to use the sequence from the parent 'aggregate' => 1, // we want to combine all CDS for this feature into a single sequence 'output_format' => 'fasta_txt', // we just want plain text, we'll format it here. 'sub_feature_types' => array('CDS'), // we're looking for CDS features '' ) ); $list_items[] = 'Coding sequence '; $sequences_html .= ''; $sequences_html .= '
'; $sequences_html .= '

Coding sequence

'; $sequences_html .= '
';
    $sequences_html .= $cds_sequence;
    $sequences_html .= '
'; $sequences_html .= 'back to top'; $sequences_html .= '
'; } // first add a list at the top of the page that can be formatted as the // user desires. We use the theme_item_list function of Drupal to create // the list rather than hard-code the HTML here. Instructions for how // to create the list can be found here: // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_item_list/7 print ''; print theme_item_list(array( 'items' => $list_items, 'title' => '', 'type' => 'ul', 'attributes' => array(), )); // now print the sequences print $sequences_html; }