if (isset($oOutput) && isset($oOutput->string)) {
$aVariantDescriptions[$zTranscript['geneid']] = $oOutput->string;
} else {
$aVariantDescriptions[$zTranscript['geneid']] = array();
}
}
$bAdded = false;
if (count($aVariantDescriptions[$zTranscript['geneid']])) {
// Loop through the mutalyzer output for this gene, see if we can find this transcript.
foreach ($aVariantDescriptions[$zTranscript['geneid']] as $key => $sVariant) {
// Check if our transcript is in the variant description for each value returned by mutalyzer.
if (!empty($sVariant) && preg_match('/^' . preg_quote($zTranscript['id_ncbi']) . ':([cn]\\..+)$/', $sVariant, $aMatches)) {
// Call the mappingInfo module of mutalyzer to get the start & stop positions of this variant on the transcript.
$aMapping = array();
try {
$oOutput = $_Mutalyzer->mappingInfo(array('LOVD_ver' => $_SETT['system']['version'], 'build' => $_CONF['refseq_build'], 'accNo' => $zTranscript['id_ncbi'], 'variant' => $aMatches[1]))->mappingInfoResult;
if (isset($oOutput->errorcode)) {
throw new Exception();
}
$aMapping = array('position_c_start' => $oOutput->startmain, 'position_c_start_intron' => $oOutput->startoffset, 'position_c_end' => $oOutput->endmain, 'position_c_end_intron' => $oOutput->endoffset);
} catch (Exception $e) {
}
if (!$aMapping) {
$aMapping = array('position_c_start' => 0, 'position_c_start_intron' => 0, 'position_c_end' => 0, 'position_c_end_intron' => 0);
}
// Insert all the gathered information about the variant description into the database.
$_DB->query('INSERT INTO ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' (id, transcriptid, position_c_start, position_c_start_intron, position_c_end, position_c_end_intron, effectid, `VariantOnTranscript/DNA`) VALUES (?, ?, ?, ?, ?, ?, ?, ?)', array($nID, $nTranscript, $aMapping['position_c_start'], $aMapping['position_c_start_intron'], $aMapping['position_c_end'], $aMapping['position_c_end_intron'], $_SETT['var_effect_default'], $aMatches[1]));
$bAdded = true;
$aGenesUpdated[] = $aTranscripts[$nTranscript];
// Speed improvement: remove this value from the output from mutalyzer, so we will not check this one again with the next transcript that we will add.
unset($aVariantDescriptions[$zTranscript['geneid']][$key]);
