Load the parents for a gff3 feature

Parameters

$feature:

$cvterm:

$parents:

$organism_id:

$fmin:

Related topics

File

tripal_feature/includes/tripal_feature.gff_loader.inc, line 1270

Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.

Code

function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, 
$organism_id, $strand, $phase, $fmin, $fmax) {

  $uname = $feature->uniquename;
  $type = $cvterm->name;
  $rel_type = 'part_of';

  // Prepare these SQL statements that will be used repeatedly.
  $cvterm_sql = "
    SELECT CVT.cvterm_id
    FROM {cvterm} CVT
      INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
      LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
    WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)
  ";

  // Iterate through the parents in the list.
  foreach ($parents as $parent) {
    // Get the parent cvterm.
    $values = array(
      'organism_id' => $organism_id,
      'uniquename' => $parent,
    );
    $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);
    if (count($result) == 0) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot find parent: %parent", array('%parent' => $parent));
      return '';
    }
    $parent_type = $result[0]->type_name;

    // try to find the parent
    $parentcvterm = chado_query($cvterm_sql, array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
    $relcvterm = chado_query($cvterm_sql, array(':cvname' => 'sequence', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
    if (!$relcvterm) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot find the term, 'part_of', from the sequence ontology. This term is used for associating parent and children features. Please check that the ontology is fully imported.");
      exit;
    }
    $values = array(
      'organism_id' => $organism_id,
      'uniquename' => $parent,
      'type_id' => $parentcvterm->cvterm_id,
    );
    $result = chado_select_record('feature', array('feature_id'), $values);
    $parent_feature = $result[0];

    // if the parent exists then add the relationship otherwise print error and skip
    if ($parent_feature) {

      // check to see if the relationship already exists
      $values = array(
        'object_id' => $parent_feature->feature_id,
        'subject_id' => $feature->feature_id,
        'type_id' => $relcvterm->cvterm_id,
      );
      $rel = chado_select_record('feature_relationship', array('*'), $values);

      if (count($rel) > 0) {
      }
      else {
        // the relationship doesn't already exist, so add it.
        $values = array(
          'subject_id' => $feature->feature_id,
          'object_id' => $parent_feature->feature_id,
          'type_id' => $relcvterm->cvterm_id,
        );
        $result = chado_insert_record('feature_relationship', $values);
        if (!$result) {
          tripal_report_error("tripal_feature", TRIPAL_WARNING, "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)", 
          array());
        }
      }

      // If this feature is a CDS and now that we know the parent we can
      // add it to the tripal_gffcds_temp table for later lookup.
      if ($type == 'CDS') {
        $values = array(
          'feature_id' => $feature->feature_id,
          'parent_id' => $parent_feature->feature_id,
          'fmin' => $fmin,
          'fmax' => $fmax,
          'strand' => $strand,
        );
        if ($phase) {
          $values['phase'] = $phase;
        }
        $result = chado_insert_record('tripal_gffcds_temp', $values);
        if (!$result) {
          tripal_report_error('tripal_feature', TRIPAL_ERROR, "Cound not save record in temporary CDS table, Cannot continue.", array());
          exit;
        }
      }
    }
    else {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent", 
      array());
    }
  }
}