Create the feature record & link it to it's analysis

Parameters

$organism:

$analysis_id:

$cvterm:

$uniquename:

$name:

$residues:

$is_analysis:

$is_obsolete:

$add_only:

$score:

Related topics

File

tripal_feature/includes/tripal_feature.gff_loader.inc, line 1704

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

Code

function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uniquename, 
$name, $residues, $is_analysis = 'f', $is_obsolete = 'f', $add_only, $score) {

  // Check to see if the feature already exists.
  $feature = NULL;
  $fselect = array(
    'organism_id' => $organism->organism_id,
    'uniquename' => $uniquename,
    'type_id' => $cvterm->cvterm_id
  );
  $columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
  $result = chado_select_record('feature', $columns, $fselect);
  if (count($result) > 0) {
    $feature = $result[0];
  }

  if (strcmp($is_obsolete, 'f') == 0 or $is_obsolete == 0) {
    $is_obsolete = 'FALSE';
  }
  if (strcmp($is_obsolete, 't') == 0 or $is_obsolete == 1) {
    $is_obsolete = 'TRUE';
  }
  if (strcmp($is_analysis, 'f') == 0 or $is_analysis == 0) {
    $is_analysis = 'FALSE';
  }
  if (strcmp($is_analysis, 't') == 0 or $is_analysis == 1) {
    $is_analysis = 'TRUE';
  }

  // Insert the feature if it does not exist otherwise perform an update.
  if (!$feature) {
    $values = array(
      'organism_id' => $organism->organism_id,
      'name' => $name,
      'uniquename' => $uniquename,
      'md5checksum' => md5($residues),
      'type_id' => $cvterm->cvterm_id,
      'is_analysis' => $is_analysis,
      'is_obsolete' => $is_obsolete,
    );
    $feature = (object) chado_insert_record('feature', $values);
    if (!$feature) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Failed to insert feature '$uniquename' ($cvterm->name)", array());
      return 0;
    }
  }
  elseif (!$add_only) {
    $values = array(
      'name' => $name,
      'md5checksum' => md5($residues),
      'is_analysis' => $is_analysis,
      'is_obsolete' => $is_obsolete,
    );
    $match = array(
      'organism_id' => $organism->organism_id,
      'uniquename' => $uniquename,
      'type_id' => $cvterm->cvterm_id,
    );
    $result = chado_update_record('feature', $match, $values);
    if (!$result) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Failed to update feature '$uniquename' ($cvterm->name)", array());
      return 0;
    }
  }
  else {
    // The feature exists and we don't want to update it so return
    // a value of 0.  This will stop all downstream property additions
    return $feature;
  }

  // Add the analysisfeature entry to the analysisfeature table if
  // it doesn't already exist.
  $af_values = array(
    'analysis_id' => $analysis_id,
    'feature_id' => $feature->feature_id
  );
  $afeature = chado_select_record('analysisfeature', array('analysisfeature_id'), $af_values);
  if (count($afeature) == 0) {
    // if a score is available then set that to be the significance field
    if (strcmp($score, '.') != 0) {
      $af_values['significance'] = $score;
    }
    if (!chado_insert_record('analysisfeature', $af_values)) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array());
    }
  }
  else {
    // if a score is available then set that to be the significance field
    $new_vals = array();
    if (strcmp($score, '.') != 0) {
      $new_vals['significance'] = $score;
    }
    else {
      $new_vals['significance'] = '__NULL__';
    }
    if (!$add_only) {
      $ret = chado_update_record('analysisfeature', $af_values, $new_vals);
      if (!$ret) {
        tripal_report_error("tripal_feature", TRIPAL_WARNING, "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array());
      }
    }
  }

  return $feature;
}