File

tripal_feature/includes/seq_extract.inc, line 457

Code

function tripal_feature_seq_extract_get_features($org_commonname, $genus, $species, $analysis_name, 
$type, $feature_name, $upstream, $downstream, $output_format, $derive_from_parent, $aggregate, 
$child, $relationship, $rel_part) {

  $sub_features = explode(',', $child);

  if (!$output_format) {
    $output_format = 'fasta_txt';
  }

  if (!$type and !$feature_name and !$genus) {
    print "Please provide a type, feature name or genus\n";
    return;
  }

  // get the list of features
  $vars = array();
  $sql = "SELECT DISTINCT F.feature_id, F.name, F.uniquename, O.genus, O.species, CVT.name as feature_type " .
    "FROM {feature} F " .
    "  INNER JOIN {organism} O on O.organism_id = F.organism_id " .
    "  INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id ";
  if ($analysis_name) {
    $sql .= "  INNER JOIN {analysisfeature} AF on AF.feature_id = F.feature_id " .
      "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ";
  }
  $sql .= "WHERE (1=1) ";
  if ($org_commonname) {
    $sql .= "AND O.common_name = '%s' ";
    $vars[] = $org_commonname;
  }
  if ($genus) {
    $sql .= "AND O.genus = '%s' ";
    $vars[] = $genus;
  }
  if ($species) {
    $sql .= "AND O.species = '%s' ";
    $vars[] = $species;
  }
  if ($type) {
    $sql .= "AND CVT.name = '%s' ";
    $vars[] = $type;
  }
  if ($feature_name) {
    if (is_array($feature_name)) {
      $sql .= "AND F.name IN (";
      foreach ($feature_name as $i => $fname) {
        $sql .= "'%s', ";
        $vars[] = $fname;
      }
      // remove the trailing comma and close the paren
      $sql = substr($sql, 0, -2) . ")";
    }
    else {
      $sql .= "AND F.name = '%s'";
      $vars[] = $feature_name;
    }
  }
  if ($analysis_name) {
    $sql .= "AND A.name = '%s'";
    $vars[] = $analysis_name;
  }
  $num_bases_per_line = 50;
  $num_seqs = 0;
  $q = chado_query($sql, $vars);

  while ($feature = db_fetch_object($q)) {

    $feature_id = $feature->feature_id;

    // build the header for each FASTA entry
    if ($feature->uniquename == $feature->name) {
      $feature_name = "$feature->uniquename $feature->feature_type ($feature->genus $feature->species)";
    }
    else {
      $feature_name = "$feature->uniquename $feature->name $feature->feature_type ($feature->genus $feature->species)";
    }

    // generate the sequence
    $sequence = tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
    $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, 
    $upstream, $downstream, $sub_features, $relationship, $rel_part);

    // print the sequence
    print $sequence;
    $num_seqs++;
  }
  if ($num_seqs == 0) {
    print "No Sequences Found";
  }
}