Load the derives from attribute for a gff3 feature

Parameters

$feature:

$subject:

$organism:

Related topics

File

tripal_feature/includes/tripal_feature.gff_loader.inc, line 1161

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

Code

function tripal_feature_load_gff3_derives_from($feature, $cvterm, $object, 
$organism, $fmin, $fmax) {

  $type = $cvterm->name;

  // First look for the object feature in the temp table to get it's type.
  $values = array(
    'organism_id' => $organism->organism_id,
    'uniquename' => $object,
  );
  $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);
  $type_id = NULL;
  if (count($result) > 0) {
    $otype = tripal_get_cvterm(array(
      'name' => $result[0]->type_name,
      'cv_id' => array(
        'name' => 'sequence'
      )
    ));
    if ($otype) {
      $type_id = $otype->cvterm_id;
    }
  }

  // If the object wasn't in the temp table then look for it in the
  // feature table and get it's type.
  if (!$type_id) {
    $result = chado_select_record('feature', array('type_id'), $values);
    if (count($result) > 1) {
      watchdog("tripal_feature", "Cannot find feature type for, '%subject' , in 'derives_from' relationship. Multiple matching features exist with this uniquename.", 
      array('%subject' => $object), WATCHDOG_WARNING);
      return '';
    }
    else if (count($result) == 0) {
      watchdog("tripal_feature", "Cannot find feature type for, '%subject' , in 'derives_from' relationship.", 
      array('%subject' => $object), WATCHDOG_WARNING);
      return '';
    }
    else {
      $type_id = $result->type_id;
    }
  }

  // Get the object feature.
  $match = array(
    'organism_id' => $organism->organism_id,
    'uniquename' => $object,
    'type_id' => $type_id,
  );
  $ofeature = chado_select_record('feature', array('feature_id'), $match);
  if (count($ofeature) == 0) {
    tripal_report_error('tripal_feature', TRIPAL_ERROR, "Could not add 'Derives_from' relationship " .
      "for %uniquename and %subject.  Subject feature, '%subject', " .
      "cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject));
    return;
  }

  // If this feature is a protein then add it to the tripal_gffprotein_temp.
  if ($type == 'protein' or $type == 'polypeptide') {
    $values = array(
      'feature_id' => $feature->feature_id,
      'parent_id' => $ofeature[0]->feature_id,
      'fmin' => $fmin,
      'fmax' => $fmax
    );
    $result = chado_insert_record('tripal_gffprotein_temp', $values);
    if (!$result) {
      tripal_report_error('tripal_feature', TRIPAL_ERROR, "Cound not save record in temporary protein table, Cannot continue.", array());
      exit;
    }
  }

  // Now check to see if the relationship already exists. If it does
  // then just return.
  $values = array(
    'object_id' => $ofeature[0]->feature_id,
    'subject_id' => $feature->feature_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => 'sequence'
      ),
      'name' => 'derives_from',
    ),
    'rank' => 0
  );
  $rel = chado_select_record('feature_relationship', array('*'), $values);
  if (count($rel) > 0) {
    return;
  }

  // finally insert the relationship if it doesn't exist
  $ret = chado_insert_record('feature_relationship', $values);
  if (!$ret) {
    tripal_report_error("tripal_feature", TRIPAL_WARNING, "Could not add 'Derives_from' relationship for $feature->uniquename and $subject", 
    array());
  }
}