Related topics

File

tripal_feature/tripal_feature.module, line 1350

@todo Add file header description

Code

function tripal_feature_get_matched_alignments($feature) {
  // This function is for features that align through an intermediate such
  // as 'EST_match' or 'match'.  This occurs in the case where two sequences
  // align but where one does not align perfectly.  Some ESTs may be in a contig
  // but not all of the EST.  Portions may overhang and not be included in the
  // consensus if quality is bad.
  // For example:
  //
  //    Feature 1: Contig --------------------
  //    Feature 2: EST_match           -------
  //    Feature 3: EST                 ---------
  //
  // The feature provided to the function will always be the feature 1.  The
  // featureloc columns prefixed with 'right' (e.g. right_fmin) belong to the
  // alignment of feature 3 with feature 2
  //
  // Features may align to more than one feature and are not matches. We do
  // not want to include these, so we have to filter on the SO terms:
  // match, or %_match
  //
  $sql = "SELECT  " .
    "   FL1.featureloc_id    as left_featureloc_id, " .
    "   FL1.srcfeature_id    as left_srcfeature_id, " .
    "   FL1.feature_id       as left_feature_id, " .
    "   FL1.fmin             as left_fmin, " .
    "   FL1.is_fmin_partial  as left_is_fmin_partial, " .
    "   FL1.fmax             as left_fmax, " .
    "   FL1.is_fmax_partial  as left_is_fmax_partial, " .
    "   FL1.strand           as left_strand,  " .
    "   FL1.phase            as left_phase, " .
    "   FL1.locgroup         as left_locgroup, " .
    "   FL1.rank             as left_rank, " .
    "   FL2.featureloc_id    as right_featureloc_id, " .
    "   FL2.srcfeature_id    as right_srcfeature_id, " .
    "   FL2.feature_id       as right_feature_id, " .
    "   FL2.fmin             as right_fmin, " .
    "   FL2.is_fmin_partial  as right_is_fmin_partial, " .
    "   FL2.fmax             as right_fmax, " .
    "   FL2.is_fmax_partial  as right_is_fmax_partial, " .
    "   FL2.strand           as right_strand,  " .
    "   FL2.phase            as right_phase, " .
    "   FL2.locgroup         as right_locgroup, " .
    "   FL2.rank             as right_rank " .
    "FROM {feature} F1 " .
    "  INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id " .
    "  INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id " .
    "  INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id " .
    "  INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id " .
    "WHERE F1.feature_id = %d " .
    "  AND (CVT2.name = 'match' or CVT2.name like '%_match') " .
    "ORDER BY FL1.fmin";

  $results = chado_query($sql, $feature->feature_id);

  // iterate through the results and add them to our featurelocs array
  $featurelocs = array();
  while ($fl = db_fetch_object($results)) {
    // ignore featurelocs where the left and right srcfeature is the same
    if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
      continue;
    }
    $featurelocs[] = $fl;
  }
  return $featurelocs;
}